Query         gi|254780182|ref|YP_003064595.1| DNA gyrase subunit A [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 910
No_of_seqs    225 out of 2407
Neff          5.8 
Searched_HMMs 39220
Date          Mon May 23 08:20:21 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780182.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01063 gyrA DNA gyrase, A s 100.0       0       0 2802.2  67.8  854   16-899     1-864 (864)
  2 PRK05560 DNA gyrase subunit A; 100.0       0       0 2463.1  86.2  814   11-909     4-817 (822)
  3 PRK13979 DNA topoisomerase IV  100.0       0       0 2378.2  84.1  855    9-902     7-912 (959)
  4 PRK05561 DNA topoisomerase IV  100.0       0       0 2157.7  74.7  734    8-842     3-743 (745)
  5 COG0188 GyrA Type IIA topoisom 100.0       0       0 2119.5  77.0  794   16-900     8-803 (804)
  6 TIGR01061 parC_Gpos DNA topois 100.0       0       0 1906.9  38.1  729   16-831     1-738 (745)
  7 TIGR01062 parC_Gneg DNA topois 100.0       0       0 1568.0  55.9  683   16-745     1-704 (747)
  8 PRK09631 DNA topoisomerase IV  100.0       0       0 1402.8  54.5  609   20-726     2-615 (626)
  9 PRK09630 DNA topoisomerase IV  100.0       0       0 1299.6  44.3  468   19-539     2-479 (479)
 10 smart00434 TOP4c DNA Topoisome 100.0       0       0 1187.1  42.3  439   19-497     1-444 (445)
 11 cd00187 TOP4c DNA Topoisomeras 100.0       0       0 1149.0  43.1  443   39-508     2-445 (445)
 12 pfam00521 DNA_topoisoIV DNA gy 100.0       0       0 1084.0  43.2  423   40-499     1-424 (428)
 13 PRK12758 DNA topoisomerase IV  100.0       0       0  887.3  55.4  695    8-830    14-729 (879)
 14 PTZ00108 DNA topoisomerase II; 100.0 2.8E-45       0  423.6  31.5  468   12-512   721-1208(1506)
 15 KOG0355 consensus              100.0 2.6E-42       0  397.7 -38.0  752   11-883    71-830 (842)
 16 PRK13979 DNA topoisomerase IV   99.9 4.9E-24 1.3E-28  234.1  22.3  240  536-833   622-948 (959)
 17 PRK05560 DNA gyrase subunit A;  99.9 7.2E-23 1.8E-27  223.7  22.3  199  535-745   608-809 (822)
 18 TIGR01063 gyrA DNA gyrase, A s  99.9 3.9E-22   1E-26  217.1  19.1  192  538-741   636-862 (864)
 19 KOG0355 consensus               99.9 1.5E-21 3.7E-26  212.0   8.2  185   17-251   645-831 (842)
 20 PRK05561 DNA topoisomerase IV   99.8 9.9E-19 2.5E-23  186.7  21.3  188  646-901   509-700 (745)
 21 COG0188 GyrA Type IIA topoisom  99.7 1.5E-15 3.9E-20  158.1  18.3   81  648-729   653-736 (804)
 22 TIGR01061 parC_Gpos DNA topois  99.5 4.9E-14 1.2E-18  144.7   8.5  199  647-901   499-705 (745)
 23 TIGR01062 parC_Gneg DNA topois  98.7 1.1E-06 2.8E-11   78.9  14.1  186  648-900   508-703 (747)
 24 PRK09631 DNA topoisomerase IV   98.1  0.0034 8.6E-08   47.7  22.7   68  653-725   458-527 (626)
 25 pfam03989 DNA_gyraseA_C DNA gy  98.0 3.3E-05 8.3E-10   65.7   7.0   47  851-897     2-48  (50)
 26 pfam03989 DNA_gyraseA_C DNA gy  97.9 6.2E-05 1.6E-09   63.2   7.0   48  693-741     1-48  (50)
 27 PRK09630 DNA topoisomerase IV   97.6  0.0059 1.5E-07   45.5  13.4  112  357-491   308-427 (479)
 28 KOG1240 consensus               96.7   0.095 2.4E-06   34.7  16.6  153  646-863  1062-1220(1431)
 29 KOG3863 consensus               87.3     2.4   6E-05   22.2   6.6   64  394-489   458-532 (604)
 30 KOG1920 consensus               87.0     2.5 6.3E-05   22.1  12.3   16  307-324   649-664 (1265)
 31 TIGR02895 spore_sigI RNA polym  85.7     2.5 6.5E-05   21.9   5.6  100  360-521    64-163 (225)
 32 pfam11197 DUF2835 Protein of u  84.8     2.9 7.5E-05   21.4   5.6   45  692-738    19-66  (68)
 33 KOG4212 consensus               82.4     1.9   5E-05   23.0   3.8   63  265-331    46-110 (608)
 34 pfam04201 TPD52 Tumour protein  81.2     3.1   8E-05   21.1   4.5   49  465-520    26-74  (162)
 35 pfam05133 Phage_prot_Gp6 Phage  80.0     4.3 0.00011   19.8   6.2   12  121-132   140-151 (435)
 36 COG5207 UBP14 Isopeptidase T [  77.1    0.67 1.7E-05   27.1   0.0   14   89-102   162-175 (749)
 37 KOG4010 consensus               76.6     5.3 0.00014   19.1   4.8   43  463-505    39-81  (208)
 38 pfam12395 DUF3658 Protein of u  75.6     1.5 3.7E-05   24.1   1.5   53   67-132    57-110 (111)
 39 PRK03992 proteasome-activating  72.0     6.6 0.00017   18.2   7.7  130  471-616     5-136 (390)
 40 pfam10977 DUF2797 Protein of u  71.6     4.4 0.00011   19.8   3.1   25  591-616    76-100 (233)
 41 pfam03982 DAGAT Diacylglycerol  71.5       1 2.6E-05   25.5  -0.2   67   30-113    13-99  (297)
 42 TIGR02515 IV_pilus_PilQ type I  70.3     5.5 0.00014   19.0   3.4   36  820-865   385-420 (464)
 43 TIGR00909 2A0306 amino acid tr  69.4     4.1  0.0001   20.1   2.6   35   52-98    316-350 (451)
 44 cd04793 LanC LanC is the cycla  68.4     7.7  0.0002   17.6   3.8   70  175-244   103-188 (382)
 45 TIGR00019 prfA peptide chain r  67.3     8.1 0.00021   17.4   9.9   46  469-514    48-96  (373)
 46 cd06461 M2_ACE Peptidase famil  63.9     6.8 0.00017   18.1   2.8   55   99-157   149-206 (477)
 47 KOG2264 consensus               62.9     9.5 0.00024   16.8   4.9   46  214-260   256-310 (907)
 48 pfam04799 Fzo_mitofusin fzo-li  62.4     9.7 0.00025   16.7   6.8   54  461-514   113-169 (171)
 49 PRK03298 hypothetical protein;  61.8     8.4 0.00021   17.3   3.0   34  678-711   119-154 (224)
 50 KOG0640 consensus               61.5      10 0.00025   16.6   8.6   24  874-897   382-405 (430)
 51 PRK10834 hypothetical protein;  61.4     3.6 9.3E-05   20.5   1.0  125   78-207    47-192 (239)
 52 KOG1764 consensus               60.4     8.5 0.00022   17.3   2.8   17  235-252    85-101 (381)
 53 COG3953 SLT domain proteins [G  60.3     3.6 9.3E-05   20.5   0.9   23  113-136    66-89  (235)
 54 KOG0243 consensus               60.1      11 0.00027   16.4   8.6   25  177-201   220-244 (1041)
 55 COG1579 Zn-ribbon protein, pos  60.0      11 0.00027   16.4  10.7   63  455-517    83-145 (239)
 56 cd07925 LigA_like_1 The A subu  59.7      11 0.00027   16.4   3.5   25  447-471    43-67  (106)
 57 TIGR02894 DNA_bind_RsfA transc  59.6      11 0.00027   16.3  10.3  105  368-521    54-159 (163)
 58 pfam01939 DUF91 Protein of unk  58.9      10 0.00026   16.6   3.0   32  678-709   120-153 (228)
 59 PHA00728 hypothetical protein   58.6      11 0.00028   16.2   3.6   66  467-545     4-69  (153)
 60 PRK13378 protocatechuate 4,5-d  58.3      11 0.00028   16.2   3.5   25  447-471    54-78  (117)
 61 COG1618 Predicted nucleotide k  58.1       8  0.0002   17.5   2.3   47  264-311     6-56  (179)
 62 pfam07914 DUF1679 Protein of u  57.9     5.4 0.00014   19.0   1.4   64  182-246   161-227 (413)
 63 COG0172 SerS Seryl-tRNA synthe  57.8      11 0.00029   16.1   8.3   80  400-514     3-86  (429)
 64 cd07921 PCA_45_Doxase_A_like S  57.7      11 0.00029   16.1   3.5   25  447-471    43-67  (106)
 65 KOG3985 consensus               57.7      11 0.00029   16.1   3.9   84  158-249    95-194 (283)
 66 TIGR01051 topA_bact DNA topois  57.6     3.1   8E-05   21.1   0.2   22  493-514   347-369 (688)
 67 KOG0291 consensus               57.2      12 0.00029   16.0  14.0  152  532-716   400-555 (893)
 68 PRK04247 hypothetical protein;  57.0      11 0.00027   16.4   2.8   35  678-712   144-180 (250)
 69 pfam01401 Peptidase_M2 Angiote  56.6     9.7 0.00025   16.7   2.5   40  467-515   195-234 (595)
 70 KOG1507 consensus               56.4     7.8  0.0002   17.6   2.0   74  453-526    48-127 (358)
 71 pfam08082 PRO8NT PRO8NT (NUC06  55.4      10 0.00026   16.5   2.5   56   49-111     4-61  (152)
 72 KOG0315 consensus               55.2      12 0.00032   15.8  10.8  107  587-712    43-155 (311)
 73 TIGR00373 TIGR00373 conserved   53.6     7.1 0.00018   18.0   1.4   12   54-65     48-59  (168)
 74 PRK13379 protocatechuate 4,5-d  53.4      13 0.00033   15.6   3.4   25  447-471    55-79  (119)
 75 PRK07773 replicative DNA helic  52.6      13 0.00034   15.5  12.1   41  851-894   776-821 (868)
 76 pfam06572 DUF1131 Protein of u  52.3      14 0.00034   15.4   4.9   31  839-869    79-112 (192)
 77 pfam01208 URO-D Uroporphyrinog  52.3      14 0.00034   15.4   4.9   29  328-356   182-210 (337)
 78 pfam03444 DUF293 Domain of unk  51.0      12 0.00031   15.8   2.3   33   49-83      2-34  (79)
 79 TIGR02687 TIGR02687 conserved   50.5      14 0.00036   15.2   2.6   11  649-659   676-687 (911)
 80 COG1426 Predicted transcriptio  50.4      14 0.00037   15.2   3.3   51  447-497    15-67  (284)
 81 TIGR00034 aroFGH phospho-2-deh  50.4      11 0.00028   16.3   2.0   30  685-714   217-247 (348)
 82 KOG1359 consensus               50.3      12 0.00031   15.9   2.2   12  170-181    56-67  (417)
 83 pfam07746 LigA Aromatic-ring-o  49.6      15 0.00037   15.1   3.4   25  447-471    28-52  (88)
 84 PRK06904 replicative DNA helic  49.6      15 0.00038   15.1   2.9   23  493-515   354-376 (472)
 85 cd07923 Gallate_dioxygenase_C   49.3      15 0.00038   15.1   3.4   25  447-471    35-59  (94)
 86 KOG3584 consensus               49.3      15 0.00038   15.1   5.2   19  496-514   326-344 (348)
 87 PRK10718 hypothetical protein;  49.1      15 0.00038   15.0   5.0   59  800-869    38-111 (191)
 88 PRK13695 putative NTPase; Prov  48.4      14 0.00035   15.3   2.3   46  265-311     5-54  (174)
 89 PRK10727 DNA-binding transcrip  48.1      14 0.00035   15.4   2.2   61   37-102    17-82  (342)
 90 TIGR02707 butyr_kinase butyrat  47.4      16  0.0004   14.8   4.9   30  868-898   296-326 (353)
 91 TIGR02386 rpoC_TIGR DNA-direct  47.1      16  0.0004   14.8   3.8   92  649-745  1111-1209(1552)
 92 COG3879 Uncharacterized protei  47.0      16 0.00041   14.8   5.8   64  469-548    58-125 (247)
 93 PRK04778 septation ring format  46.2      16 0.00042   14.7  13.9   28  105-139   151-178 (569)
 94 pfam06160 EzrA Septation ring   46.2      16 0.00042   14.7  14.2   20  348-367   301-320 (559)
 95 pfam07798 DUF1640 Protein of u  46.1      16 0.00042   14.7   6.0   38  448-491    99-136 (177)
 96 cd04618 CBS_pair_5 The CBS dom  46.0      13 0.00033   15.7   1.8   69   46-116     6-85  (98)
 97 COG2949 SanA Uncharacterized m  45.2      14 0.00036   15.2   1.9  151   52-208    35-207 (235)
 98 pfam05400 FliT Flagellar prote  45.2      17 0.00043   14.6   3.4   42  479-520    60-101 (109)
 99 pfam01255 Prenyltransf Putativ  45.0      17 0.00043   14.6   3.4   64  445-517    50-113 (222)
100 pfam02650 HTH_WhiA Sporulation  44.7      17 0.00044   14.5   4.3   38  277-320    41-78  (191)
101 PRK05595 replicative DNA helic  43.9      18 0.00045   14.4   3.3   23  493-515   331-353 (444)
102 KOG4248 consensus               43.8      18 0.00045   14.4   3.8   34  128-161   268-302 (1143)
103 COG2312 Erythromycin esterase   43.7     7.2 0.00018   17.9   0.2   48   73-130    43-92  (405)
104 PRK06266 transcription initiat  42.5      18 0.00045   14.4   2.1   14  317-330    47-60  (178)
105 PRK05431 seryl-tRNA synthetase  42.4      18 0.00047   14.2  11.0   82  401-512     4-89  (422)
106 cd02639 R3H_RRM R3H domain of   42.2      18 0.00047   14.2   2.5   21   48-68     25-46  (60)
107 PRK05729 valS valyl-tRNA synth  42.2      18 0.00047   14.2   5.0   53   54-116   155-211 (877)
108 cd04585 CBS_pair_ACT_assoc2 Th  42.1      18 0.00047   14.2   3.1   75   41-117    26-110 (122)
109 pfam04849 HAP1_N HAP1 N-termin  42.0      19 0.00047   14.2   5.4   45  470-514   244-288 (307)
110 pfam10168 Nup88 Nuclear pore c  41.9      19 0.00047   14.2  11.1   11  380-390   563-573 (717)
111 COG0305 DnaB Replicative DNA h  41.6      19 0.00048   14.2   3.2   54  189-243     1-54  (435)
112 cd04600 CBS_pair_HPP_assoc Thi  41.6      19 0.00048   14.2   2.5   28   90-117    10-37  (124)
113 COG4939 Major membrane immunog  41.2      19 0.00048   14.1   3.2   47  106-152    62-113 (147)
114 PRK08082 consensus              41.1      19 0.00049   14.1   3.1   22  494-515   335-356 (453)
115 cd04469 S1_Hex1 S1_Hex1: Hex1,  40.4      17 0.00044   14.5   1.7   16  236-251    39-54  (75)
116 COG2524 Predicted transcriptio  40.1      20  0.0005   14.0   2.2   23  721-743   200-222 (294)
117 pfam04637 Herpes_pp85 Herpesvi  39.8      20 0.00051   13.9   4.6  180  163-371    66-255 (502)
118 KOG1684 consensus               39.8      12  0.0003   16.0   0.8   15   89-103    66-80  (401)
119 KOG0428 consensus               39.5      20 0.00051   13.9   3.2   10  112-121   123-132 (314)
120 PRK05617 enoyl-CoA hydratase;   39.4      19 0.00048   14.1   1.8   30  176-205   175-205 (356)
121 pfam03131 bZIP_Maf bZIP Maf tr  39.3      20 0.00051   13.9   5.6   37  470-513    55-91  (95)
122 cd03677 MM_CoA_mutase_beta Coe  39.3      20 0.00051   13.9   2.0   23  264-286   181-203 (424)
123 cd03823 GT1_ExpE7_like This fa  39.0      20 0.00052   13.8   2.4   12  231-242   148-159 (359)
124 COG3253 ywfI Predicted heme pe  38.7     9.2 0.00024   16.9   0.1   11  263-273   178-188 (230)
125 KOG2941 consensus               38.5      21 0.00053   13.8   3.4   30   68-98    152-181 (444)
126 PRK08840 replicative DNA helic  38.2      21 0.00053   13.7   3.2   23  493-515   349-371 (464)
127 TIGR01465 cobM_cbiF precorrin-  38.1      13 0.00033   15.6   0.8   14   89-102    80-93  (252)
128 pfam10458 Val_tRNA-synt_C Valy  38.0      21 0.00053   13.7   4.5   34  468-501     4-37  (66)
129 cd04603 CBS_pair_KefB_assoc Th  38.0      15 0.00039   14.9   1.2   86   30-120    12-103 (111)
130 cd04597 CBS_pair_DRTGG_assoc2   37.8      21 0.00054   13.7   3.7   69   49-117    31-101 (113)
131 pfam00465 Fe-ADH Iron-containi  37.7      21 0.00054   13.7   2.2   26  182-207    51-76  (312)
132 pfam03266 DUF265 Protein of un  37.6      21 0.00054   13.7   2.6   45  266-311     2-50  (168)
133 PRK11147 ABC transporter ATPas  37.6      21 0.00054   13.7   6.2   11  201-211   167-177 (632)
134 cd04629 CBS_pair_16 The CBS do  37.2      14 0.00036   15.3   0.9   32   89-120     8-40  (114)
135 cd04617 CBS_pair_4 The CBS dom  37.2      14 0.00036   15.3   0.9   38   78-116    60-102 (118)
136 pfam11802 CENP-K Centromere-as  37.2      22 0.00055   13.6   8.5   62  447-510    52-129 (273)
137 COG1791 Uncharacterized conser  37.1      22 0.00055   13.6   7.3  117  471-636    17-152 (181)
138 PRK10240 undecaprenyl pyrophos  37.0      22 0.00055   13.6   3.2   58  446-512    50-107 (229)
139 pfam12552 DUF3741 Protein of u  37.0      22 0.00055   13.6   2.2   39  183-225     8-46  (46)
140 pfam06838 Alum_res Aluminium r  36.7      22 0.00056   13.6   3.6   14   52-65     26-39  (405)
141 TIGR00683 nanA N-acetylneurami  36.0      22 0.00057   13.5   3.1   51  233-296   111-161 (294)
142 KOG0650 consensus               35.9      22 0.00057   13.5   7.7   50  501-555   347-410 (733)
143 cd04639 CBS_pair_26 The CBS do  35.6      23 0.00058   13.4   2.8   40   78-117    58-99  (111)
144 cd07642 BAR_ASAP2 The Bin/Amph  35.5      23 0.00058   13.4   3.3   68  451-518    83-160 (215)
145 TIGR01341 aconitase_1 aconitat  35.5      15 0.00039   14.9   0.8   74  810-898   795-874 (896)
146 TIGR03268 methan_mark_3 putati  35.5      23 0.00058   13.4   4.5  170  702-890   269-466 (503)
147 KOG3029 consensus               35.4      23 0.00058   13.4   3.3   45  170-225   136-180 (370)
148 TIGR01750 fabZ beta-hydroxyacy  35.4      12 0.00031   15.8   0.3   28  620-647    21-49  (142)
149 pfam08672 APC2 Anaphase promot  35.3      23 0.00058   13.4   3.6   36  184-219     3-41  (60)
150 KOG0787 consensus               35.3      23 0.00058   13.4   8.6   44  477-520   129-173 (414)
151 pfam11892 DUF3412 Domain of un  35.3      22 0.00055   13.6   1.6   57   45-105    28-103 (123)
152 TIGR03449 mycothiol_MshA UDP-N  35.2      23 0.00058   13.4   2.5   18  190-207   229-246 (405)
153 cd07321 Extradiol_Dioxygenase_  34.9      23 0.00059   13.3   4.0   26  447-472    33-58  (77)
154 PRK09458 pspB phage shock prot  34.8      23 0.00059   13.3   2.3   25  471-495    45-69  (75)
155 KOG4649 consensus               34.8      23 0.00059   13.3   9.2   28  798-825   250-280 (354)
156 TIGR01090 apt adenine phosphor  34.2      15 0.00038   15.1   0.6   51  192-251    28-80  (175)
157 PTZ00233 variable surface prot  34.2      18 0.00046   14.3   1.0   39  477-515    31-74  (509)
158 KOG0596 consensus               34.2      24  0.0006   13.3   2.3   10  219-228   215-224 (677)
159 PTZ00156 60S ribosomal protein  33.8      24 0.00061   13.2   1.7   61   47-118    40-102 (172)
160 pfam00356 LacI Bacterial regul  33.7      24 0.00061   13.2   2.3   35   32-68     11-46  (46)
161 COG0216 PrfA Protein chain rel  33.7      24 0.00061   13.2   6.0   45  470-514    48-94  (363)
162 PRK12806 flagellin; Provisiona  33.6      24 0.00061   13.2   6.9   62  386-488    57-127 (475)
163 KOG1302 consensus               33.4      24 0.00062   13.2   3.5   16   47-62     15-30  (600)
164 cd00225 API3 Ascaris pepsin in  33.3      24 0.00062   13.1   3.6   41  460-500    26-66  (159)
165 TIGR02171 Fb_sc_TIGR02171 Fibr  33.3      24 0.00062   13.1   5.0  166  503-679   222-410 (982)
166 TIGR03300 assembly_YfgL outer   33.1      25 0.00063   13.1  11.1   59  535-603    64-122 (377)
167 COG0493 GltD NADPH-dependent g  33.0      19 0.00049   14.1   1.0  130  219-378   112-250 (457)
168 pfam07569 Hira TUP1-like enhan  32.9      25 0.00063   13.1   5.0   27  579-609    16-42  (219)
169 KOG3091 consensus               32.9      25 0.00063   13.1  12.4   95  374-518   354-453 (508)
170 cd07603 BAR_ACAPs The Bin/Amph  32.6      25 0.00063   13.1   3.8   30  453-482    83-112 (200)
171 PRK07004 replicative DNA helic  32.4      25 0.00064   13.0   3.7   23  493-515   344-366 (460)
172 cd07924 PCA_45_Doxase_A The A   32.2      25 0.00064   13.0   6.9   25  447-471    51-75  (121)
173 KOG3957 consensus               32.1      23 0.00058   13.4   1.2   27  223-249   152-181 (387)
174 PHA02126 hypothetical protein   31.9      23 0.00057   13.5   1.2   50  224-273    50-107 (153)
175 TIGR01052 top6b DNA topoisomer  31.6      22 0.00056   13.5   1.1   15  303-317   172-186 (662)
176 cd04637 CBS_pair_24 The CBS do  31.4      26 0.00066   12.9   2.3   41   76-117    67-110 (122)
177 pfam02624 YcaO YcaO-like famil  31.4      22 0.00057   13.5   1.1   78  123-208    47-136 (332)
178 cd04605 CBS_pair_MET2_assoc Th  31.4      24 0.00062   13.2   1.3   27   91-117    11-37  (110)
179 KOG0319 consensus               31.4      26 0.00066   12.9  16.5  183  531-739   331-523 (775)
180 PRK00969 hypothetical protein;  31.4      26 0.00066   12.9   4.5  171  702-890   272-469 (508)
181 pfam08657 DASH_Spc34 DASH comp  31.3      26 0.00066   12.9   5.5   26  202-227    36-61  (212)
182 COG1293 Predicted RNA-binding   31.1      26 0.00067   12.9   5.5   42  457-498   364-407 (564)
183 PRK07778 consensus              31.1      26 0.00067   12.9   2.2   13   91-103    46-58  (386)
184 pfam06447 consensus             31.1      26 0.00067   12.9   7.8   64  447-510    46-111 (407)
185 pfam04967 HTH_10 HTH DNA bindi  31.0      26 0.00067   12.8   3.4   34   49-83      1-34  (53)
186 COG3394 Uncharacterized protei  30.8      26 0.00067   12.8   4.9  140   48-210    13-176 (257)
187 KOG3314 consensus               30.8      26 0.00067   12.8   2.7   38   51-88     38-75  (194)
188 pfam05565 Sipho_Gp157 Siphovir  30.8      26 0.00067   12.8   5.4   65  474-538    53-125 (162)
189 PRK08760 replicative DNA helic  30.7      27 0.00068   12.8   3.0   19  497-515   363-381 (476)
190 pfam03853 YjeF_N YjeF-related   30.7      25 0.00064   13.1   1.3  116   91-228    14-143 (170)
191 cd04962 GT1_like_5 This family  30.6      27 0.00068   12.8   1.9   35  481-515   324-358 (371)
192 PRK11303 DNA-binding transcrip  30.5      27 0.00068   12.8   2.7  181   37-242    16-206 (330)
193 COG3959 Transketolase, N-termi  30.5      27 0.00068   12.8   3.1   16   86-101    32-47  (243)
194 KOG0275 consensus               30.3      27 0.00068   12.8  12.3   28  840-867   439-466 (508)
195 PRK04028 glutamyl-tRNA(Gln) am  30.2      27 0.00069   12.8   8.4   70  398-511   443-514 (631)
196 pfam11629 Mst1_SARAH C termina  30.2      27 0.00069   12.7   1.9   32  486-520    12-43  (49)
197 COG1637 Predicted nuclease of   30.1      27 0.00069   12.7   3.1   14  730-743   202-215 (253)
198 PRK13377 protocatechuate 4,5-d  29.9      27 0.00069   12.7   6.9   25  447-471    54-78  (129)
199 pfam06952 PsiA PsiA protein. T  29.8      27  0.0007   12.7   2.6   16  177-192    49-64  (238)
200 cd04626 CBS_pair_13 The CBS do  29.8      22 0.00057   13.5   0.9   27   91-117    10-36  (111)
201 TIGR02483 PFK_mixed phosphofru  29.8      27  0.0007   12.7   2.9   31  260-292   197-227 (339)
202 pfam01768 Birna_VP4 Birnavirus  29.8      13 0.00033   15.6  -0.3   24  108-131    14-38  (264)
203 KOG4288 consensus               29.5      28  0.0007   12.7   3.6   35  189-240   243-277 (283)
204 KOG3686 consensus               29.4      28 0.00071   12.6   2.0   22  691-712   532-553 (740)
205 PRK13670 hypothetical protein;  29.2      27  0.0007   12.7   1.3  120   77-226     3-138 (390)
206 cd04613 CBS_pair_SpoIVFB_EriC_  29.1      24 0.00061   13.2   0.9   28   90-117     9-36  (114)
207 cd04593 CBS_pair_EriC_assoc_ba  29.0      24  0.0006   13.3   0.9   26   91-116    10-35  (115)
208 smart00116 CBS Domain in cysta  29.0      26 0.00067   12.9   1.1   30   88-117     6-35  (49)
209 COG3546 Mn-containing catalase  28.6      28 0.00073   12.5   1.3   33  117-149    29-64  (277)
210 KOG3809 consensus               28.5      29 0.00073   12.5   7.7   42  461-502   532-581 (583)
211 TIGR01122 ilvE_I branched-chai  28.4      22 0.00056   13.5   0.7   22  652-673   196-219 (302)
212 KOG4318 consensus               28.4      29 0.00073   12.5   6.7  178   25-243   194-392 (1088)
213 PRK08694 consensus              28.3      29 0.00073   12.5   3.2   23  493-515   350-372 (468)
214 pfam12529 Xylo_C Xylosyltransf  28.3      29 0.00073   12.5   1.3   41  647-687    85-125 (180)
215 KOG2052 consensus               28.2      27 0.00069   12.7   1.1   16  696-711   354-369 (513)
216 PRK11387 S-methylmethionine tr  27.8      29 0.00075   12.4   2.1   40  175-214   201-240 (465)
217 TIGR01951 nusB transcription a  27.8      29 0.00075   12.4   5.5   54  461-523    78-133 (140)
218 KOG3441 consensus               27.7      13 0.00034   15.5  -0.6   16  848-863   102-117 (149)
219 pfam05110 AF-4 AF-4 proto-onco  27.6      29 0.00075   12.4   9.3   35  372-406   909-947 (1154)
220 PRK10803 hypothetical protein;  27.5      30 0.00075   12.4   6.3   41  471-511    64-104 (262)
221 TIGR00630 uvra excinuclease AB  27.5      30 0.00075   12.4   1.4  136  128-289    49-227 (956)
222 PRK11622 putative ABC transpor  27.5      30 0.00075   12.4   1.5   38  189-240   168-205 (401)
223 PRK10423 transcriptional repre  27.5      30 0.00076   12.4   2.1  176   37-243    14-202 (327)
224 KOG2911 consensus               27.4      30 0.00076   12.4   9.6   89  387-509   289-383 (439)
225 PRK02304 adenine phosphoribosy  27.2      24 0.00061   13.2   0.7   11  731-741   139-149 (174)
226 KOG0533 consensus               27.2      30 0.00076   12.3   3.3   25  264-288    84-108 (243)
227 TIGR01037 pyrD_sub1_fam dihydr  27.2      30 0.00076   12.3   2.5   85  221-315    11-101 (308)
228 pfam09517 RE_Eco29kI Eco29kI r  27.1      24 0.00061   13.2   0.7   20   94-116   102-122 (170)
229 cd04621 CBS_pair_8 The CBS dom  27.0      30 0.00077   12.3   1.5   26   91-116    10-35  (135)
230 TIGR02303 HpaG-C-term 4-hydrox  26.9      30 0.00077   12.3   1.8   16  586-601    35-50  (249)
231 cd04635 CBS_pair_22 The CBS do  26.9      26 0.00067   12.8   0.9   28   89-116    82-109 (122)
232 KOG0005 consensus               26.9      23 0.00059   13.4   0.5   20   46-65     33-52  (70)
233 PRK08227 aldolase; Validated    26.7      30 0.00078   12.3   3.7   23  293-315   153-175 (291)
234 pfam11853 DUF3373 Protein of u  26.5      31 0.00078   12.3   2.9   20  469-488    32-51  (485)
235 TIGR01194 cyc_pep_trnsptr cycl  26.5      31 0.00078   12.3   3.2   41  303-344   104-144 (555)
236 PRK05748 replicative DNA helic  26.5      31 0.00078   12.2   3.7   22  494-515   336-357 (448)
237 KOG0216 consensus               26.4      31 0.00078   12.2   4.4  113  222-343    65-196 (1111)
238 COG4746 Uncharacterized protei  26.3      31 0.00079   12.2   2.2   28  214-245    10-37  (80)
239 PRK00202 nusB transcription an  26.3      31 0.00079   12.2   7.4   28  496-523    96-123 (132)
240 KOG0977 consensus               26.2      31 0.00079   12.2  13.4   46  473-518   294-339 (546)
241 PRK06835 DNA replication prote  26.1      31 0.00079   12.2   1.1   20   20-39     40-59  (330)
242 PRK02753 DNA-directed RNA poly  25.8      31  0.0008   12.2   1.2   14  371-384    13-26  (74)
243 KOG1446 consensus               25.8      31  0.0008   12.1  12.7   72  789-869   191-263 (311)
244 pfam05636 DUF795 Protein of un  25.7      31  0.0008   12.1   1.3  122   77-227     3-140 (389)
245 TIGR03531 selenium_SpcS O-phos  25.7      32  0.0008   12.1   4.0   98   24-145    12-113 (444)
246 pfam10985 DUF2805 Protein of u  25.7      32  0.0008   12.1   3.7   38  397-463     1-38  (73)
247 KOG4437 consensus               25.7      32  0.0008   12.1   5.1   15  319-333   149-163 (482)
248 TIGR01363 strep_his_triad stre  25.7      32 0.00081   12.1   1.5  163  526-725    61-253 (376)
249 COG1363 FrvX Cellulase M and r  25.5      32 0.00081   12.1   7.6  101  476-599     3-110 (355)
250 cd04801 CBS_pair_M50_like This  25.3      31 0.00079   12.2   1.0   23   92-114    77-99  (114)
251 pfam11552 DUF3230 Protein of u  25.3      32 0.00082   12.1   1.3   21  184-208    13-33  (105)
252 PRK08026 flagellin; Validated   25.3      32 0.00082   12.1   6.9   62  386-488    57-127 (566)
253 pfam05718 Pox_int_trans Poxvir  25.3      32 0.00082   12.1   2.4   35  451-491   348-382 (383)
254 CHL00144 odpB pyruvate dehydro  25.2      26 0.00067   12.8   0.6   44  311-363   232-277 (326)
255 pfam10480 ICAP-1_inte_bdg Beta  25.2      32 0.00082   12.1   3.9   39  786-825    97-135 (200)
256 PRK00464 nrdR transcriptional   25.2      32 0.00082   12.1   5.0   25  447-471    98-122 (149)
257 TIGR01219 Pmev_kin_ERG8 phosph  25.1      32 0.00082   12.1   3.7  141  455-617   346-497 (499)
258 PRK09492 treR trehalose repres  25.1      32 0.00082   12.0   2.5   71   31-103    15-90  (315)
259 PRK10401 DNA-binding transcrip  25.0      32 0.00082   12.0   2.5   52   32-85     13-69  (346)
260 cd04777 HTH_MerR-like_sg1 Heli  25.0      32 0.00083   12.0   6.0   47  446-492    53-105 (107)
261 cd04803 CBS_pair_15 The CBS do  24.9      31  0.0008   12.2   0.9   32   89-120     8-40  (122)
262 TIGR01055 parE_Gneg DNA topois  24.7      22 0.00055   13.6   0.1   61   44-117    10-84  (647)
263 pfam05889 SLA_LP_auto_ag Solub  24.7      33 0.00084   12.0   3.2   32  482-513   268-299 (389)
264 pfam05904 DUF863 Plant protein  24.6      27  0.0007   12.7   0.6   12  449-460   522-533 (730)
265 KOG0240 consensus               24.6      33 0.00084   12.0  10.6   56  455-510   416-477 (607)
266 TIGR03643 conserved hypothetic  24.5      33 0.00084   12.0   4.0   39  396-463     1-39  (72)
267 TIGR02817 adh_fam_1 zinc-bindi  24.4      20  0.0005   14.0  -0.2   12  113-125   241-252 (338)
268 TIGR01967 DEAH_box_HrpA ATP-de  24.2      33 0.00085   11.9   1.3   27  360-386  1139-1168(1320)
269 PRK09413 insertion sequence 2   24.2      33 0.00085   11.9   5.1   38  474-511    70-107 (121)
270 cd04612 CBS_pair_SpoIVFB_EriC_  24.2      30 0.00076   12.4   0.7   10   92-101    74-83  (111)
271 TIGR00345 arsA arsenite-activa  24.2      33 0.00085   11.9   2.2   29  468-496   199-227 (330)
272 cd04619 CBS_pair_6 The CBS dom  24.1      33 0.00085   11.9   1.6   25   90-114    75-99  (114)
273 TIGR02742 TrbC_Ftype type-F co  24.1      28 0.00071   12.6   0.5   14   89-102   107-120 (139)
274 PRK04885 ppnK inorganic polyph  24.1      33 0.00085   11.9   1.5   46  490-550     5-50  (265)
275 TIGR01334 modD modD protein; I  24.1      33 0.00085   11.9   4.3   75  345-460   146-228 (277)
276 TIGR02030 BchI-ChlI magnesium   24.0      18 0.00046   14.3  -0.5  143  188-377    60-226 (340)
277 KOG3011 consensus               23.9      34 0.00086   11.9   2.7   37  129-166   105-142 (293)
278 COG0241 HisB Histidinol phosph  23.7      21 0.00054   13.7  -0.1   50  174-229    51-100 (181)
279 PRK08006 replicative DNA helic  23.7      34 0.00087   11.8   3.0   12  214-225    49-60  (471)
280 pfam06530 Phage_antitermQ Phag  23.6      34 0.00087   11.8   1.2   37  180-216    25-70  (126)
281 COG4800 Predicted transcriptio  23.6      34 0.00087   11.8   2.5   78  208-290    38-123 (170)
282 PRK06819 flagellin; Validated   23.6      34 0.00087   11.8   7.3   22  466-487   104-125 (371)
283 PRK07263 consensus              23.5      34 0.00087   11.8   3.3   23  493-515   334-356 (453)
284 PRK08411 flagellin; Reviewed    23.4      34 0.00088   11.8   6.8   62  386-488    57-127 (573)
285 TIGR00501 met_pdase_II methion  23.4      16 0.00042   14.7  -0.8   38  676-716   205-244 (327)
286 PHA02094 hypothetical protein   23.2      35 0.00088   11.8   1.0   20   71-90     43-62  (81)
287 TIGR00444 mazG MazG family pro  23.1      20 0.00052   13.8  -0.3   15  471-485   163-177 (253)
288 PRK13588 flagellin B; Provisio  23.1      35 0.00089   11.8   6.8   63  386-489    57-128 (514)
289 pfam12226 Astro_capsid_p Turke  23.0      35 0.00089   11.7   2.8   17  676-692   120-136 (230)
290 PRK11462 putative transporter;  23.0      35 0.00089   11.7   1.7   28  456-483   421-448 (460)
291 cd04631 CBS_pair_18 The CBS do  23.0      34 0.00085   11.9   0.8   28   90-117     9-37  (125)
292 KOG4777 consensus               22.9      35 0.00089   11.7   1.2  111   84-213    25-154 (361)
293 PRK13729 conjugal transfer pil  22.7      35  0.0009   11.7   7.6   59  446-509    59-117 (474)
294 PRK04184 DNA topoisomerase VI   22.7      21 0.00054   13.7  -0.3   36  301-337   165-203 (533)
295 pfam04762 IKI3 IKI3 family. Me  22.6      35  0.0009   11.7   9.6   28  680-707   526-553 (918)
296 TIGR02938 nifL_nitrog nitrogen  22.5      36 0.00091   11.7   0.9   10  598-607   371-380 (496)
297 COG1110 Reverse gyrase [DNA re  22.5      36 0.00091   11.7   5.6   70   70-140    67-150 (1187)
298 PRK12756 phospho-2-dehydro-3-d  22.5      36 0.00091   11.7   2.0   22  119-142    62-83  (349)
299 PRK11747 dinG ATP-dependent DN  22.5      36 0.00091   11.7   7.5   21   42-62     17-39  (697)
300 KOG3347 consensus               22.5      36 0.00091   11.7   2.9   37  264-302     8-44  (176)
301 TIGR01916 F420_puta_dedox F420  22.4      32 0.00081   12.1   0.6  120  595-734    51-191 (260)
302 cd00475 CIS_IPPS Cis (Z)-Isopr  22.3      36 0.00092   11.6   2.6   20  385-404    21-40  (221)
303 TIGR02768 TraA_Ti Ti-type conj  22.2      36 0.00092   11.6   2.8   43  644-686   500-543 (888)
304 PRK10977 hypothetical protein;  22.2      36 0.00092   11.6   3.7   59  140-212    48-107 (510)
305 PRK13355 bifunctional HTH-doma  22.2      36 0.00092   11.6   2.6   90  193-297   215-319 (518)
306 COG4026 Uncharacterized protei  22.2      36 0.00092   11.6   5.1   43  471-513   159-201 (290)
307 CHL00191 ycf61 DNA-directed RN  22.2      36 0.00092   11.6   1.2   17  369-385    11-27  (74)
308 PRK10869 recombination and rep  22.1      36 0.00092   11.6  10.9   12  459-470   302-313 (553)
309 pfam00534 Glycos_transf_1 Glyc  22.1      36 0.00092   11.6   1.5   21  190-210   140-160 (172)
310 pfam00768 Peptidase_S11 D-alan  22.1      36 0.00092   11.6   3.2   84   45-145    84-168 (241)
311 pfam07426 Dynactin_p22 Dynacti  22.0      36 0.00093   11.6   7.9   19  477-495    97-115 (172)
312 COG0576 GrpE Molecular chapero  21.9      36 0.00093   11.6   7.1   50  499-548   121-176 (193)
313 TIGR03604 docking_ocin bacteri  21.9      36 0.00093   11.6   2.7   54  149-208    72-136 (377)
314 KOG2896 consensus               21.9      37 0.00093   11.6  12.5  111  358-492    54-169 (377)
315 TIGR01034 metK S-adenosylmethi  21.8      30 0.00077   12.3   0.4   16  176-191   120-135 (393)
316 PRK00927 tryptophanyl-tRNA syn  21.8      37 0.00093   11.6   9.2  115  318-513   208-324 (325)
317 COG2039 Pcp Pyrrolidone-carbox  21.7      37 0.00094   11.5   1.1   19  190-208    40-58  (207)
318 KOG4577 consensus               21.6      37 0.00094   11.5   1.3   54  461-520   199-252 (383)
319 pfam06609 TRI12 Fungal trichot  21.6      31 0.00079   12.2   0.4   32   28-59     53-84  (598)
320 cd04588 CBS_pair_CAP-ED_DUF294  21.6      36 0.00092   11.6   0.7   68   40-117    25-98  (110)
321 PRK10548 flagellar biosynthesi  21.6      37 0.00094   11.5   3.4   52  485-536    66-118 (121)
322 pfam05615 THOC7 Tho complex su  21.5      37 0.00094   11.5  10.7   70  446-516    53-127 (135)
323 TIGR02404 trehalos_R_Bsub treh  21.5      30 0.00077   12.3   0.3  147  214-376     7-163 (236)
324 KOG0998 consensus               21.4      37 0.00095   11.5   4.6   52  468-519   505-556 (847)
325 PRK11779 sbcB exonuclease I; P  21.4      37 0.00095   11.5  12.4   48  308-356   256-313 (477)
326 pfam02827 PKI cAMP-dependent p  21.4      33 0.00083   12.0   0.4   23   26-48      4-28  (74)
327 KOG2303 consensus               21.3      37 0.00095   11.5   4.1   40  281-328   373-413 (706)
328 cd04768 HTH_BmrR-like Helix-Tu  21.3      37 0.00095   11.5   4.5   40  447-490    56-95  (96)
329 PRK10580 proY putative proline  21.3      37 0.00095   11.5   2.0   39  176-214   195-233 (457)
330 pfam09220 LA-virus_coat L-A vi  21.1      28 0.00071   12.6   0.1   67  297-364   201-282 (436)
331 PRK12808 flagellin; Provisiona  21.1      38 0.00096   11.5   6.9   62  386-488    55-125 (460)
332 KOG0306 consensus               21.1      38 0.00096   11.4  12.3   93  643-736   464-565 (888)
333 pfam08961 DUF1875 Domain of un  21.0      38 0.00096   11.4   5.5   40  449-488   123-163 (243)
334 cd04775 HTH_Cfa-like Helix-Tur  21.0      38 0.00096   11.4   5.7   45  447-491    56-101 (102)
335 PRK09109 motC flagellar motor   21.0      38 0.00097   11.4   1.2   26  276-301    73-98  (246)
336 COG4168 SapB ABC-type antimicr  21.0      38 0.00097   11.4   1.0  105   52-207     5-118 (321)
337 cd04642 CBS_pair_29 The CBS do  20.9      38 0.00097   11.4   1.0   25   91-115    10-34  (126)
338 COG1675 TFA1 Transcription ini  20.8      38 0.00097   11.4   1.9   14  205-218    27-40  (176)
339 COG0082 AroC Chorismate syntha  20.8      31 0.00079   12.2   0.2   64  325-390     6-70  (369)
340 TIGR01296 asd_B aspartate-semi  20.7      30 0.00075   12.4   0.1   58  840-900   240-314 (350)
341 pfam09417 consensus             20.7      38 0.00098   11.4   3.3   13  448-460   108-120 (121)
342 KOG0207 consensus               20.6      38 0.00098   11.4   3.1   26  379-404   233-258 (951)
343 TIGR00058 Hemerythrin hemeryth  20.6      37 0.00093   11.6   0.6   42  352-395    40-83  (116)
344 PRK06321 replicative DNA helic  20.6      39 0.00098   11.4   3.6   22  494-515   360-381 (472)
345 TIGR02976 phageshock_pspB phag  20.5      39 0.00098   11.4   3.0   25  471-495    45-69  (75)
346 pfam09942 DUF2174 Uncharacteri  20.5      31 0.00078   12.2   0.2   13  105-117    25-37  (83)
347 pfam02502 LacAB_rpiB Ribose/Ga  20.5      35 0.00089   11.8   0.4   40  338-379    99-138 (140)
348 PRK05469 peptidase T; Provisio  20.5      39 0.00098   11.4   4.6   59  153-211    94-161 (405)
349 TIGR01992 PTS-IIBC-Tre PTS sys  20.3      39 0.00099   11.3   2.6   51  193-244    15-74  (489)
350 PRK10703 DNA-binding transcrip  20.3      39 0.00099   11.3   2.6   46   37-83     17-67  (335)
351 COG5184 ATS1 Alpha-tubulin sup  20.3      39 0.00099   11.3  11.8   18  689-706   236-253 (476)
352 PRK00574 gltX glutamyl-tRNA sy  20.3      39 0.00099   11.3   4.4   17   53-69     56-72  (489)
353 PRK10334 mechanosensitive chan  20.3      25 0.00064   13.0  -0.3   35  172-209    95-129 (285)
354 KOG2230 consensus               20.2      39   0.001   11.3   0.8   39  189-231   161-201 (867)
355 PRK06223 malate dehydrogenase;  20.2      39   0.001   11.3   3.0   35  454-491   277-311 (312)
356 KOG1891 consensus               20.1      38 0.00097   11.4   0.6   25  497-521   233-257 (271)
357 PRK12584 flagellin A; Reviewed  20.1      39   0.001   11.3   6.7   62  386-488    57-127 (510)
358 PRK11706 TDP-4-oxo-6-deoxy-D-g  20.1      39   0.001   11.3   4.5   21  281-301   135-155 (375)
359 pfam08820 DUF1803 Domain of un  20.0      39   0.001   11.3   3.4   11  505-515    31-41  (94)
360 PRK09848 glucuronide transport  20.0      39   0.001   11.3   3.4   31  458-488   422-452 (457)

No 1  
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=2802.17  Aligned_cols=854  Identities=51%  Similarity=0.842  Sum_probs=810.7

Q ss_pred             EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             66600999998767877799886313754000897367899999998789999981134042556643668870478999
Q gi|254780182|r   16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD   95 (910)
Q Consensus        16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~   95 (910)
                      |.|++|++||++|||+|||||||||||||||||||||||||||||+++||+||+|||||||||||||||||||||+||||
T Consensus         1 i~pv~ie~E~k~SYLdYAMSVIVsRALPDvRDGLKPVHRRiLYaM~~~Gl~~d~~~kKsARIVGDV~GkYHPHGD~aiYD   80 (864)
T TIGR01063         1 IVPVNIEEEMKRSYLDYAMSVIVSRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDVLGKYHPHGDSAIYD   80 (864)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCEEEEEECCCCCCCCCCHHHH
T ss_conf             94565788999998644111322211541003688504577667766278998866002428741047824898734676


Q ss_pred             HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCH
Q ss_conf             99971220111561314788708877697201357899978999999863076840533068988548503432273211
Q gi|254780182|r   96 ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVL  175 (910)
Q Consensus        96 a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL  175 (910)
                      ||||||||||||||||||||||||||||||||||||||||+|+|++||+|||||||||+||||||++||+||||+|||||
T Consensus        81 ~LVRMAQDFSlRYpLvDGQGNFGSiDGD~pAAMRYTEaRl~k~a~~ll~DIdKeTVdF~~NYDg~~~EP~VLPs~fPnLL  160 (864)
T TIGR01063        81 ALVRMAQDFSLRYPLVDGQGNFGSIDGDPPAAMRYTEARLTKIAEELLRDIDKETVDFVPNYDGSEKEPTVLPSRFPNLL  160 (864)
T ss_pred             HHHHHCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             77650587100354416888647888882676521788888999999862043631654488886258820751241456


Q ss_pred             HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEE
Q ss_conf             01676101013317898547899999988761877688888863458668874434475889999870120389999886
Q gi|254780182|r  176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSH  255 (910)
Q Consensus       176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~  255 (910)
                      ||||||||||||||||||||+||||||+++|+||+||++|||++||||||||||+|+|++||++||+||||||+||||+|
T Consensus       161 vNGSsGIAVGMATNIPPHNL~Eiida~~~~i~Np~~~i~eLl~~i~GPDFPTgg~I~G~~GI~~AY~TGRG~i~~Rar~~  240 (864)
T TIGR01063       161 VNGSSGIAVGMATNIPPHNLGEIIDAILAYIDNPDISIEELLEVIKGPDFPTGGIILGRSGIREAYETGRGSIVIRARAE  240 (864)
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCHHHHHCCCCCHHHHHHCCCCEEEEEEEEE
T ss_conf             13247600022257887336899999999871899886799560771137105643050013777335881389999899


Q ss_pred             EEECCC--CCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHC-CCCCEEEEEEECCCCCHHHHHHHHHHHCC
Q ss_conf             543367--845999924644352899999999998716650144587303-74655799994798877899999997610
Q gi|254780182|r  256 IEKTSG--DREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDES-DRQGYRVVIELKRGASADVILNQLYRYTS  332 (910)
Q Consensus       256 ie~~~~--~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeS-dr~giRivielKr~~~~~~vln~Lyk~T~  332 (910)
                      ||+.++  ||.+||||||||||||++|||||||||++|||+||||||||| ||+|||||||+|||+.|++|||+|||+|+
T Consensus       241 iE~~~~~~gR~~IIvTE~PYqVNKa~LiekIAeLv~ek~ieGIsdiRDESSDr~GiRiVIE~KRD~~a~VvLN~LYk~T~  320 (864)
T TIGR01063       241 IEEDSKKGGREAIIVTEIPYQVNKARLIEKIAELVREKKIEGISDIRDESSDREGIRIVIELKRDAVAEVVLNNLYKQTQ  320 (864)
T ss_pred             EEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHCCCC
T ss_conf             98648899862488862888520268889999874000000321244256687743799997428983015421211264


Q ss_pred             HHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH
Q ss_conf             11000000245541663000299999999999999999999999999988877899999987406999999861899789
Q gi|254780182|r  333 LQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPET  412 (910)
Q Consensus       333 Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~e  412 (910)
                      ||++||+|||||++|.|++|+||++|.+|++||++||+|||.|+|+||++|+||||||++|++||||||+|||+|++++.
T Consensus       321 lQ~~Fg~NmLALv~G~Pk~lnLk~~l~~f~~HR~~Vi~RRT~feLrKA~eRaHiL~GL~~AL~niDevI~lIr~S~~~~~  400 (864)
T TIGR01063       321 LQVSFGINMLALVDGLPKVLNLKELLEAFVEHRKDVITRRTIFELRKAEERAHILEGLLIALDNIDEVIALIRASQNTEE  400 (864)
T ss_pred             CCEECCEEEEEEECCCCCEECHHHHHHHHHHCCEEEEEEEHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             50014812321107897501788999999842313355210001022655789999999999721289999742789889


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             87877631269788999997402211122234452369999999998789999888799999989999999998875304
Q gi|254780182|r  413 ARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILS  492 (910)
Q Consensus       413 Ak~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~  492 (910)
                      ||..|+++.|....+..++...  ........+.|.|||.||+|||||||||||+||.+||++||++|.++|++|++||+
T Consensus       401 Ak~~L~e~~W~l~di~~ll~~~--~~~~l~~~g~F~l~E~QA~AILdMrL~rLTgLE~~Kl~~E~~~L~~~I~~l~~iL~  478 (864)
T TIGR01063       401 AKTRLVERQWELLDILPLLKLV--LEVELGERGTFSLSEIQAQAILDMRLQRLTGLEREKLEEEYKELLELIADLEDILA  478 (864)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHH--HHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9988421686078999999887--67532888865448899999999887677888899999999999999999997503


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCEEECC-CCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9899999999989999984056883310013-434530101456781899907970523310000023345652110001
Q gi|254780182|r  493 SRSRLLGIIKQELLSVKDELDTPRRTRIVEG-LLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVM  571 (910)
Q Consensus       493 s~~~l~~iI~~EL~eik~kygd~RRT~I~~~-~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~  571 (910)
                      |+.+++++|++||.+|+++|||||||+|+.+ ...++.||||.+|+||||||++|||||+|+++|++|+|||||++|+++
T Consensus       479 ~~~r~~~iireEL~~i~~~Fgd~RRT~I~~~~~~~~D~EDLI~~E~vVvt~s~~GYvKR~p~~~Y~~Q~RGGkG~~g~~~  558 (864)
T TIGR01063       479 SEERVLEIIREELEEIKEQFGDPRRTEIVAEESEDIDIEDLIARENVVVTLSHKGYVKRVPVSAYRSQKRGGKGVSGADL  558 (864)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCHHHHCCCCEEEEEECCCEEEECCHHHHHCCCCCCCCCCCCCC
T ss_conf             77689999999999999973885321222024322450344147878999716864786030133257666646432531


Q ss_pred             CC-CCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEE
Q ss_conf             46-41010113323777399995489399982000432244456554124545-36556200256630125666871799
Q gi|254780182|r  572 RD-EDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILS-LNQGERITTIMPFPEDESSWNNLYVV  649 (910)
Q Consensus       572 ke-~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lv  649 (910)
                      ++ +||+.++|+|+|||+||||||+|||||+|||+||+++|++||.||.|||+ +.++|+|++++|+++|+....+.|||
T Consensus       559 ~~G~D~i~~~lvasTHD~~Lfftn~G~vY~lK~Y~iP~~~R~akG~pIvNLL~G~~~dE~I~ai~~v~~f~d~~~~~yl~  638 (864)
T TIGR01063       559 KDGDDFIEQLLVASTHDYLLFFTNRGKVYRLKVYQIPEASRTAKGKPIVNLLEGLQKDERITAILSVKEFEDEAYDLYLF  638 (864)
T ss_pred             CCCCCEEEEEEEEECCCEEEEEECCCCEEEEEEEECCCCCCCCCCCHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEEE
T ss_conf             23685056778830776078881888268645441787775678712888605787676688873566668552661799


Q ss_pred             EEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCE-EEEEECCCEEEEEEHH--HCCCCCCCCCCCEEE
Q ss_conf             9947991898423686204777227866158985788896189826-9999369859997587--623547866553576
Q gi|254780182|r  650 FATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQEND-ILLTTKLGQCVRFPIS--AIRVFAGRNSVGVRG  726 (910)
Q Consensus       650 l~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~-Iil~T~~G~~lrF~~~--evr~~~GR~a~GVkg  726 (910)
                      |+|++|.|||++|++|.++|++|++||+|+|||+|++|.+|.++++ |+|+|++|+++||+.+  +||+| ||+|+||+|
T Consensus       639 ~aTk~G~vKk~~L~~F~~~rs~GiiAi~L~e~D~L~~v~~~~~~~~~v~l~s~~G~~~RF~~~~~~vR~m-gR~~~GV~G  717 (864)
T TIGR01063       639 LATKNGVVKKTSLTEFSNIRSNGIIAIKLDEGDELISVRLVDGDDEKVMLGSKNGKAVRFPEEDEEVREM-GRATRGVRG  717 (864)
T ss_pred             EECCCCEEEEEECHHHHHHHHCCEEEEEEECCCEEEEEEEEECCCCEEEEEECCCCEEECCCCCCCHHCC-CCCCCCEEE
T ss_conf             9726743887400144354527869999708968999999607886588651488479836885311002-455676013


Q ss_pred             EECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC-EEEEEEC
Q ss_conf             752899869998973366654200000122233333334555444444443332222232001110125686-7999975
Q gi|254780182|r  727 ISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQ-FILTVSE  805 (910)
Q Consensus       727 IkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~-~IL~vTe  805 (910)
                      |+|+.+|.|+++.++..-.+--+++                         +..+...+...-.......++. +||+||+
T Consensus       718 i~L~~~~~v~~~~~~~~i~~~~~D~-------------------------~~~~L~~NlD~vv~~~~~~e~~~~lL~vt~  772 (864)
T TIGR01063       718 IKLKNEDSVISMTVLKGINSIKEDR-------------------------NLEELGVNLDFVVSLEVVSEESQKLLIVTE  772 (864)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHH-------------------------HHHHCCCCEEEEEEEEEECCCCCEEEEEEE
T ss_conf             5406777400013443212002222-------------------------465437424344777862499837899830


Q ss_pred             CCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEE
Q ss_conf             99345301788486675774148876067777686899997289964999945998999990105544515687388980
Q gi|254780182|r  806 KGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFST  885 (910)
Q Consensus       806 ~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L  885 (910)
                      |||||||++++||.|+|||+||++++++++  +|.||++.+|.++|+||++|+.|++||+.+.+||++||+||||||++|
T Consensus       773 nGyGKRt~~~~yr~~~RGg~Gv~~~~~~~r--~G~vVga~~V~~~d~lm~iT~~G~~iR~~~~~vs~~GR~t~GVrL~~l  850 (864)
T TIGR01063       773 NGYGKRTSIEEYRLQSRGGKGVKSIKITDR--NGQVVGAIAVDDDDELMLITSSGKLIRTSVQDVSIQGRNTQGVRLIRL  850 (864)
T ss_pred             CCCCEECCHHHCCCCCCCCCEEEEEEEECC--CCCEEEEEEECCCCHHHHEECCCCEEEEEEEHHCCCCCCCCCEEEEEE
T ss_conf             684200426257632656623788998646--896878987458740001010883799761032115653565589851


Q ss_pred             CCCCEEEEEEEECC
Q ss_conf             89987999998356
Q gi|254780182|r  886 AKDERVVSVERIRE  899 (910)
Q Consensus       886 ~~~D~Vv~va~i~~  899 (910)
                      +++|+|++|+++++
T Consensus       851 ~e~d~vv~v~~~~~  864 (864)
T TIGR01063       851 DEDDKVVSVSLVAK  864 (864)
T ss_pred             CCCCCEEEEEECCC
T ss_conf             78763564220279


No 2  
>PRK05560 DNA gyrase subunit A; Validated
Probab=100.00  E-value=0  Score=2463.11  Aligned_cols=814  Identities=55%  Similarity=0.922  Sum_probs=798.2

Q ss_pred             CCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCH
Q ss_conf             43235666009999987678777998863137540008973678999999987899999811340425566436688704
Q gi|254780182|r   11 EEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGN   90 (910)
Q Consensus        11 ~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd   90 (910)
                      ...++|++++|++||++|||+||||||++||||||||||||||||||||||+|||+|++||+||||||||||||||||||
T Consensus         4 ~~~~~i~~~~~~~~~~~~yl~Ya~svi~~RAlPdvrDGlKPv~RRily~M~~l~l~~~~~~~K~ArivG~v~gkyHPHGd   83 (822)
T PRK05560          4 ELADRIIPVNIEEEMKRSYLDYAMSVIVGRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDVMGKYHPHGD   83 (822)
T ss_pred             HHHCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCCCC
T ss_conf             03344445348999998899888999985128864468850899999999872899999974420664100547789882


Q ss_pred             HHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCC
Q ss_conf             78999999712201115613147887088776972013578999789999998630768405330689885485034322
Q gi|254780182|r   91 AAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCAR  170 (910)
Q Consensus        91 ~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~  170 (910)
                      +|||||||||||+|+||||||||||||||+||||||||||||||||++|++||+||+++||||+||||||++||+||||+
T Consensus        84 ~siY~alvrmaQ~~~~r~plidg~GNfGsidgd~~AAmRYTE~rl~~~~~~ll~di~~~tV~f~~NfD~s~~EP~vLPa~  163 (822)
T PRK05560         84 SAVYDALVRMAQDFSLRYPLVDGQGNFGSIDGDPAAAMRYTEARLAKIAHELLRDIDKETVDFVPNYDGSEQEPTVLPAR  163 (822)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             17999999970022304732715788889999800666678888799999998511306525504889876586525656


Q ss_pred             CCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEE
Q ss_conf             73211016761010133178985478999999887618776888888634586688744344758899998701203899
Q gi|254780182|r  171 YPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVI  250 (910)
Q Consensus       171 ~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~i  250 (910)
                      |||||||||+|||||||||||||||+||||||++||+||++++++||+|||||||||||+|+|.+||++||+||||||++
T Consensus       164 ~PnlLvNGs~GIAVGmATniPpHNL~Evi~a~~~~i~np~~t~~~L~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~i  243 (822)
T PRK05560        164 FPNLLVNGSSGIAVGMATNIPPHNLGEVIDACLALIDNPDITIEELMEIIPGPDFPTGGIILGRSGIREAYRTGRGSIIM  243 (822)
T ss_pred             CCHHHCCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCEEEECCHHHHHHHHHCCCEEEE
T ss_conf             64532057751002110588996889999999986359999999994669899799982897848799999837670999


Q ss_pred             EEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             99886543367845999924644352899999999998716650144587303746557999947988778999999976
Q gi|254780182|r  251 RGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRY  330 (910)
Q Consensus       251 R~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~  330 (910)
                      ||||++|+.++||++||||||||||||++|||+||+||++|||+||+||||||||+||||||||||+++|++|||+||||
T Consensus       244 R~k~~iE~~~~~r~~IvItEIPY~vnk~~liekIa~lv~~kki~gI~dirDESdr~GiRIVIelKr~~~~~~vln~Lyk~  323 (822)
T PRK05560        244 RAKAEIEEIRKGREAIIVTEIPYQVNKARLIEKIAELVKEKKIEGISDIRDESDRDGMRIVIELKRDAVPEVVLNNLYKH  323 (822)
T ss_pred             EEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHH
T ss_conf             88999998579953899996898577999999999998557544510300356877627999967989979999999860


Q ss_pred             CCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             10110000002455416630002999999999999999999999999999888778999999874069999998618997
Q gi|254780182|r  331 TSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNP  410 (910)
Q Consensus       331 T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~  410 (910)
                      |+||+||++||+||++|+|++|||+++|++|++||++||+||++|+|+||++|+||||||++|++|||+||+|||+|+|+
T Consensus       324 T~Lq~sf~~N~~al~~g~P~~l~Lk~~L~~fi~hR~~vi~rr~~~~L~ka~~RlhIleGl~~a~~~iDeVI~iIR~S~~~  403 (822)
T PRK05560        324 TQLQTSFGINMLALVDGQPKLLNLKQILEAFVDHRKEVITRRTRFELRKARERAHILEGLLIALDNIDEVIALIRASPTP  403 (822)
T ss_pred             CCHHHCCCCEEEEEECCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCH
T ss_conf             84132036117998799877864999999999999999999999999999988999988999995879999999718987


Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89878776312697889999974022111222344523699999999987899998887999999899999999988753
Q gi|254780182|r  411 ETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDI  490 (910)
Q Consensus       411 ~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~I  490 (910)
                      ++||.+||++                          |+|||.||+|||+|||||||+||+++|++|+++|.++|++|++|
T Consensus       404 ~~Ak~~L~~~--------------------------f~lse~QA~AIL~mrL~rLt~Le~~kl~~E~~eL~~~I~~l~~I  457 (822)
T PRK05560        404 AEAREGLMER--------------------------YGLSEIQAQAILDMRLQRLTGLEREKIEDEYKELLAEIADLLDI  457 (822)
T ss_pred             HHHHHHHHHH--------------------------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999989887--------------------------58899999999998999987678999999999999999999988


Q ss_pred             HCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             04989999999998999998405688331001343453010145678189990797052331000002334565211000
Q gi|254780182|r  491 LSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVV  570 (910)
Q Consensus       491 L~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~  570 (910)
                      |+|+++++++|++||.+++++|||||||+|.++.++++.||+|++|+++|++|+.|||||+|+++|++|+|||||+++++
T Consensus       458 L~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~ei~~EDLI~~E~vvVtlS~~GYIKR~~~~~yr~Q~RGGkG~~g~~  537 (822)
T PRK05560        458 LASPERLMEIIREELEEIKEKFGDPRRTEIEAGEGDIDDEDLIANEDVVVTLTHGGYIKRVPLDEYRAQRRGGKGKSGAG  537 (822)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCHHHCCCCCCEEEEEECCCEEEEECHHHHHHHCCCCCCCCCCC
T ss_conf             65999999999999999999829988604415656562544177764699994682688613266553126777743430


Q ss_pred             CCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEE
Q ss_conf             14641010113323777399995489399982000432244456554124545365562002566301256668717999
Q gi|254780182|r  571 MRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVF  650 (910)
Q Consensus       571 ~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl  650 (910)
                      +|++|++.++|.|+|||+||||||.|||||++||+||+++|+++|+||.||+++.++|+|++++++++++   ++.||+|
T Consensus       538 ~ke~D~v~~~~~~~Thd~LLfFTn~Grvy~lkv~eIPe~sr~skG~~i~nll~l~~~EkI~ail~v~~~~---~~~~Lv~  614 (822)
T PRK05560        538 TKEDDFVEHLFVANTHDTLLFFTNRGRVYRLKVYELPEGSRTAKGRPIVNLLPLEPGEKITAILPVREFD---DDLYLFF  614 (822)
T ss_pred             CCCCCHHHHEEEECCCCEEEEEECCCCEEEEEEEECCCCCCCCCCCCHHHHCCCCCCCEEEEEEECCCCC---CCCEEEE
T ss_conf             4556534432682478879999369949998916745668777884899716899997367877125678---8856999


Q ss_pred             EECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECC
Q ss_conf             94799189842368620477722786615898578889618982699993698599975876235478665535767528
Q gi|254780182|r  651 ATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLA  730 (910)
Q Consensus       651 ~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~  730 (910)
                      +|++|+|||+++++|.+++++|++||+|++||+|++|.+++++++|+++|++|++|||++++||+| ||+|+||+||+|+
T Consensus       615 ~Tk~G~IKRt~L~df~~~r~~G~~AikLke~DeLv~v~l~~~~~dIil~T~~G~alRF~~~eVR~~-GR~a~GVkgIkL~  693 (822)
T PRK05560        615 ATKNGTVKKTALSEFSNIRSNGLIAINLDEGDELIGVRLTDGDDDVLLFSANGKAIRFPEEDVRPM-GRTARGVRGIKLR  693 (822)
T ss_pred             EECCCCEEEECHHHCCCCCCCCEEEEECCCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCC-CCCCCCCCCEECC
T ss_conf             957972797136872255525519998589977999998489987999978973999506657777-8877684315519


Q ss_pred             CCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEE
Q ss_conf             99869998973366654200000122233333334555444444443332222232001110125686799997599345
Q gi|254780182|r  731 KGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEKGFGK  810 (910)
Q Consensus       731 ~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GK  810 (910)
                      ++|+||||.++.+                                                     +++||+||++||||
T Consensus       694 ~gD~VV~~~vv~~-----------------------------------------------------~~~iL~vTe~G~GK  720 (822)
T PRK05560        694 EGDEVVSMSVLRD-----------------------------------------------------EQFVLTVTENGYGK  720 (822)
T ss_pred             CCCEEEEEEEECC-----------------------------------------------------CCEEEEEECCCEEE
T ss_conf             9998999998579-----------------------------------------------------98799991898053


Q ss_pred             EEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCCCE
Q ss_conf             30178848667577414887606777768689999728996499994599899999010554451568738898089987
Q gi|254780182|r  811 RTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKDER  890 (910)
Q Consensus       811 Rt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~D~  890 (910)
                      ||++++||.|+|||+||++|+++++  +|.||+++.|+++||||++|++|++||+++++||++||+||||++|+|+++|+
T Consensus       721 Rt~~~eyr~~~RGgkGv~~ik~~~k--~G~lv~~~~V~~~deI~liT~~G~~iRi~v~~I~~~gR~t~GVrl~~L~~~d~  798 (822)
T PRK05560        721 RTPAEEYRLQGRGGKGVIAIKITER--NGKLVGAVPVDDDDEIMLITDAGKLIRTRVSEIRITGRNTQGVTLIRLDEGEK  798 (822)
T ss_pred             ECCHHHCCCCCCCCCCEEEEEECCC--CCCEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCEEEEECCCCCE
T ss_conf             0528883755778777588996488--88489999917998699992798799987100475675788708998599998


Q ss_pred             EEEEEEECCCCCCCCCCCC
Q ss_conf             9999983566555665557
Q gi|254780182|r  891 VVSVERIRESEIVDEAEST  909 (910)
Q Consensus       891 Vv~va~i~~~e~~de~e~~  909 (910)
                      |++|++|++++++++.+.+
T Consensus       799 v~~va~v~~~~~~~~e~~~  817 (822)
T PRK05560        799 VVSVARVAEEEEEEEEEGE  817 (822)
T ss_pred             EEEEEEECCCCCCCCCCCC
T ss_conf             9999980787665445544


No 3  
>PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated
Probab=100.00  E-value=0  Score=2378.21  Aligned_cols=855  Identities=36%  Similarity=0.551  Sum_probs=779.8

Q ss_pred             CCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCC
Q ss_conf             76432356660099999876787779988631375400089736789999999878999998113404255664366887
Q gi|254780182|r    9 DEEEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPH   88 (910)
Q Consensus         9 ~~~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPH   88 (910)
                      +=|.+++|++++|++||++|||+||||||++||||||||||||||||||||||+||++|++||+||||||||||||||||
T Consensus         7 ~~p~~~~i~~~~i~~em~~syl~YamsVI~~RAlPDvRDGLKPVhRRiLy~M~~lg~~~~~~~~KsArivGdv~GkyHPH   86 (959)
T PRK13979          7 VIPKDNNIIKFPLEEAMPENYLPYAVEVAKDRALPDVRDGLKPVHRRILYGAYMLKAFPDKPYYKSARIVGDILGKYHPH   86 (959)
T ss_pred             CCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCCCC
T ss_conf             78986875561489999988998889987750077644688518999999998738999999841235511026477898


Q ss_pred             CHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECC
Q ss_conf             04789999997122011156131478870887769720135789997899999986307684053306898854850343
Q gi|254780182|r   89 GNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLC  168 (910)
Q Consensus        89 Gd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP  168 (910)
                      ||+|||||||||||+||||||||||||||||+||||||||||||||||++|++||.|||++||||+||||||++||+|||
T Consensus        87 GD~avYdalVrmaQ~fs~r~pLidgqGNfGSidgD~~AAmRYTEarl~~~a~~ll~di~k~tVdf~~NyD~s~~EP~VLP  166 (959)
T PRK13979         87 GDSSVYDAMVILAQNFTTRMPLIDGHGNWGSIDGDSAAAMRYTEARLTPIAMEMLRDIDKDVVDMVDNYSDSEKEPKVLP  166 (959)
T ss_pred             CCHHHHHHHHHHHCCHHHCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             70479999999700013127606067867899998103430688888999999983304277476148898876865135


Q ss_pred             CCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEE
Q ss_conf             22732110167610101331789854789999998876187768888886345866887443447588999987012038
Q gi|254780182|r  169 ARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSI  248 (910)
Q Consensus       169 ~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i  248 (910)
                      |+|||||||||+|||||||||||||||+||||||++||+||++++++||+|||||||||||+|+|.+||++||+||||+|
T Consensus       167 a~~PnLLvNGs~GIAVGMATnIPpHNL~Evida~~a~i~np~~t~~eLm~~i~GPDFPTGGiI~g~~gi~~aY~TGrG~i  246 (959)
T PRK13979        167 ARYPNLLVNGAFGIAVGLATNIPPHNLKEVIDGTLAYIDNNEITTKELMNYIKGPDLPTGGILIGKKSLLSAYETGEGKV  246 (959)
T ss_pred             CCCCHHHHCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCEEECCHHHHHHHHHCCCEE
T ss_conf             77743221377401141225879978899999999997089988999982187998899848988787999998489839


Q ss_pred             EEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCC----CCHHHHHHHHCCCCCEEEEEEECCCCCHH---
Q ss_conf             99998865433678459999246443528999999999987166----50144587303746557999947988778---
Q gi|254780182|r  249 VIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKR----IVDIADLRDESDRQGYRVVIELKRGASAD---  321 (910)
Q Consensus       249 ~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~k----i~gI~dirDeSdr~giRivielKr~~~~~---  321 (910)
                      ++||||++|+.++||++||||||||||||++|+|+||+||++||    |+||+|+||||||+||||||||||+++|+   
T Consensus       247 ~iRak~~iE~~~~gr~~IiItEiPY~vnka~lie~Iaelv~~kk~~k~i~gIsdiRDESDr~GiRIVIelKr~a~~~v~e  326 (959)
T PRK13979        247 TLRAKTTIEKLENGRLGIVITEFPYRRNKAKLLQTISEMTADKKHSKALENISDIRDESDRNGIRAVIEFKKSADEDVAE  326 (959)
T ss_pred             EEEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHH
T ss_conf             99988899961788448999966875778999999999997131336688600420136778638999976889757699


Q ss_pred             HHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999997610110000002455416630002999999999999999999999999999888778999999874069999
Q gi|254780182|r  322 VILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVV  401 (910)
Q Consensus       322 ~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI  401 (910)
                      +|||+|||||+||+||++||+||++|+|++|||+++|++|++||++||+|||+|+|+||++|+||||||++|++|||+||
T Consensus       327 ~vLn~Lyk~T~LQ~sf~vNmlaL~~g~P~~l~Lk~iL~~fl~hR~eVI~RRt~~~L~ka~~R~HILeGL~iAl~nIDevI  406 (959)
T PRK13979        327 KVLKYLYKKTDLQCNISFNMVALADGKPETMGLKAIIKHYVEHQKEVVTRRTKKELEIAEKRFHIVEGFIKAIGIMDEII  406 (959)
T ss_pred             HHHHHHHHHCCCCEEEEEEEEEECCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH
T ss_conf             99999997498836774589973399134977899999999999999999999999889989999998999997899999


Q ss_pred             HHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99861899789878776312697889999974022111222344523699999999987899998887999999899999
Q gi|254780182|r  402 RIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLG  481 (910)
Q Consensus       402 ~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~  481 (910)
                      +|||+|+++++||.+||++                          |+|||.||+|||+|||||||+||++||++|+++|.
T Consensus       407 ~iIR~S~~~~~Ak~~L~~~--------------------------f~lse~QA~AILdmrL~rLT~LE~~ki~~E~~eL~  460 (959)
T PRK13979        407 KTIRASKSKKDASENLIEK--------------------------FGFTDEQAEAILELMLYRLTGLEIKVFEKEYKELE  460 (959)
T ss_pred             HHHHCCCCHHHHHHHHHHH--------------------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9998189837999989876--------------------------19999999999998999987889999999999999


Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCC--CCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCC
Q ss_conf             9999887530498999999999899999840568833100134--34530101456781899907970523310000023
Q gi|254780182|r  482 IEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGL--LDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQ  559 (910)
Q Consensus       482 ~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~--~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q  559 (910)
                      ++|++|++||+|+++++++|++||.+++++|||||||+|+++.  .+++.||||++|+++||+|+.|||||+|+++|   
T Consensus       461 ~~I~~l~~IL~s~~~l~~iIk~EL~eik~kygd~RRT~Ii~~~~~~~~~~EDLI~~EdvVVtlS~~GYIKR~pl~~Y---  537 (959)
T PRK13979        461 KLIKKLEKILSSEKELLKVIKKELKEVKEKYGDERRTSIIEDDEKAKIDIEELIVVEDVVITLSNEGFIKRIPLKSY---  537 (959)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHCCCCCEEEEEECCCEEEECCHHHH---
T ss_conf             99999999967999999999999999999839987426665632033657673456655999806964750458881---


Q ss_pred             CCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEEC--CCCCCEEEEEEEC
Q ss_conf             34565211000146410101133237773999954893999820004322444565541245453--6556200256630
Q gi|254780182|r  560 RRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSL--NQGERITTIMPFP  637 (910)
Q Consensus       560 ~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l--~~~E~I~ail~~~  637 (910)
                      +|||+|..|+.++|+|++.++|.|+|||+||||||.|+|||+++|+||+++|++||+||.|++++  .++|+|+++++++
T Consensus       538 ~RgGkG~~g~~~ke~D~v~~l~~a~THd~lLfFTn~GkvY~lKvyeIPe~sr~aKG~~i~Nll~~l~l~~E~I~~il~v~  617 (959)
T PRK13979        538 NRSNSNVEDIEYREGDFNKFLIQSNTKDTLLIFTDKGNMYQIKGINIPEFKWKEKGERLDEIIKTIDLEEEKIIEAYSIE  617 (959)
T ss_pred             CCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEECCCEEEEEEEEECCCCCCCCCCCCHHHHCCCCCCCCCEEEEEEECC
T ss_conf             36789977875556651026899528963999957985999870566777700389573441055788984589977412


Q ss_pred             CCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCE---EEEEECCCEEEEEEHHHCC
Q ss_conf             1256668717999947991898423686204777227866158985788896189826---9999369859997587623
Q gi|254780182|r  638 EDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQEND---ILLTTKLGQCVRFPISAIR  714 (910)
Q Consensus       638 ~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~---Iil~T~~G~~lrF~~~evr  714 (910)
                      +|.   ++.||+|+|++|+||||++++| +.+++|++||+|++||+|++|.+++++++   |++.|++|+++||+++++|
T Consensus       618 ~f~---~~~~lvfaTk~G~VKKt~L~~f-~~~~sgiiAIkL~egDeLI~V~l~~~~~~~~~i~l~T~~G~~irf~e~~vR  693 (959)
T PRK13979        618 DFT---PQKDFIFITDSGGIKKTSLDKF-NTNYSKLMALKLKKGEELIKVKLVDRTREEKFLKIKTKKGLSFTVEEPELE  693 (959)
T ss_pred             CCC---CCCEEEEEECCCEEECCCHHHC-CCCCCCCEEEECCCCCEEEEEEEECCCCCCEEEEEECCCCEEEECCCHHCC
T ss_conf             267---7754999928986883738982-855678366666999879878973588875079996589659971420224


Q ss_pred             CCCCCCCCCEEEEECCCCCEEEEEEEECCCCCCCCCC-------CCCCC--C---------CCC---CCCCCCCCCCCCC
Q ss_conf             5478665535767528998699989733666542000-------00122--2---------333---3333455544444
Q gi|254780182|r  715 VFAGRNSVGVRGISLAKGDQVISMAIVLHADADYDER-------ICYMK--H---------MSA---QRRLISGDTEEIT  773 (910)
Q Consensus       715 ~~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~-------~~~~~--~---------~~~---~~~~~~~~~~~~~  773 (910)
                      +| ||+|+||+||+|+++|+||+|.++.+.+......       .....  .         .+.   ......+.+...+
T Consensus       694 ~m-GR~a~GVrgi~L~~~D~Vvsm~i~~~~e~~~~~~~i~~~g~i~~~~~~~~~~~~~~~~~~~~~ili~~~~G~~~~~~  772 (959)
T PRK13979        694 PV-DRNILGYQLFNLSPNDSIKKVDFCDNYEYKEFYININKKGIIKISDLKKNKSHISLKTNSSKNLLLFSDKGKVYKIP  772 (959)
T ss_pred             CC-CCCCCCEEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEECCCCCEEECC
T ss_conf             57-87666752143399998986102244420000023342002332210011111111356631135432577233032


Q ss_pred             -----CCCCC----------CCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCC
Q ss_conf             -----44433----------322222320011101256867999975993453017884866757741488760677776
Q gi|254780182|r  774 -----SLKND----------SSVEGNISEERCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGKGIRATDVSKINEI  838 (910)
Q Consensus       774 -----~~~~~----------~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~  838 (910)
                           ...+.          .................++.++|++|++||||||+++|||.++|||+|++..     +++
T Consensus       773 ~~~~~~~~~~g~~i~~~~~~~~~~e~vi~~~~~~~~~e~~~il~vTe~G~GKRT~~~eyr~~g~~~~~~k~~-----~~~  847 (959)
T PRK13979        773 AFMLQNIEESGINISALTGDFEKKESIINAISIFEFEEDLSIYFFSKKGLVKKTLLSEFKGEGNSTQVYKFK-----HKE  847 (959)
T ss_pred             HHHCCCCCCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEEEE-----ECC
T ss_conf             432023355564502222121022302466520357776159999358974666567733467864899988-----448


Q ss_pred             CCEEEE-EECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCCCEEEEEEEECCCCC
Q ss_conf             868999-9728996499994599899999010554451568738898089987999998356655
Q gi|254780182|r  839 GALVAV-FPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKDERVVSVERIRESEI  902 (910)
Q Consensus       839 g~lv~~-~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~D~Vv~va~i~~~e~  902 (910)
                      |.+|++ +.++++|+||++|++|++||+++++|+++||+||||++++|+++|+|++++++.+++.
T Consensus       848 ~~~v~~~~~~~~~d~imliT~~G~~IR~~v~~I~~~GR~tqGV~li~L~~~dkVV~~~~i~~~~~  912 (959)
T PRK13979        848 DELVSVDINEHEQKNILIITKKGMAIRFKSEAVNPMGKIASGVTGISLKDEDKVIFGSIIDENDT  912 (959)
T ss_pred             CCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCEEEEECCCCCEEEEEEEECCCCC
T ss_conf             97899997048996389990798799987243470260368806897389987999999747777


No 4  
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=100.00  E-value=0  Score=2157.71  Aligned_cols=734  Identities=41%  Similarity=0.654  Sum_probs=698.8

Q ss_pred             CCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCC
Q ss_conf             87643235666009999987678777998863137540008973678999999987899999811340425566436688
Q gi|254780182|r    8 SDEEEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHP   87 (910)
Q Consensus         8 ~~~~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHP   87 (910)
                      .-++..++|++++|++||++|||+||||||++||||||||||||||||||||||+||++|++||+|||||||||||||||
T Consensus         3 ~~~~~~e~i~~~~~~~~~~~~yl~Ya~svi~~RalPd~rDGlKPv~RRily~m~~~~l~~~~~~~KsarivG~v~GkyHP   82 (745)
T PRK05561          3 MPDPMSEGIEDLPLEEFLEERYLRYSMYVIMDRALPDVRDGLKPVQRRILYAMSELGLTPDAKFKKSARTVGDVLGKYHP   82 (745)
T ss_pred             CCCCHHCCCEEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEEHHHCCCCCC
T ss_conf             99832058157238999998899989999985127764458860999999999972899999973631664100557789


Q ss_pred             CCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEEC
Q ss_conf             70478999999712201115613147887088776972013578999789999998630768405330689885485034
Q gi|254780182|r   88 HGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVL  167 (910)
Q Consensus        88 HGd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vl  167 (910)
                      |||+|||||||||||+|+||||||||||||||+||||||||||||||||++|++||+|||++||||+||||||++||+||
T Consensus        83 HGD~siY~a~vrmaQ~f~~r~plidg~GNfGsidgd~~AAmRYTE~rls~~~~~~l~di~~~tv~f~~n~D~~~~EP~vL  162 (745)
T PRK05561         83 HGDSAIYDAMVRMAQDFSYRYPLVDGQGNFGSIDGDPAAAMRYTEARLSKIAELLLEEIDEGTVDFVPNFDGTLEEPTVL  162 (745)
T ss_pred             CCHHHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEE
T ss_conf             87047999999973301315751427887789999843767889887699999999630647513205879997675543


Q ss_pred             CCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCC-CCCHHHHHHHHHHCCC
Q ss_conf             322732110167610101331789854789999998876187768888886345866887443-4475889999870120
Q gi|254780182|r  168 CARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAV-ILGRTGIKNAYATGRG  246 (910)
Q Consensus       168 P~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~-I~~~~~i~~~y~tGrG  246 (910)
                      ||+|||||||||+|||||||||||||||+||||||++||+||++++++||+|||||||||||+ |.|++||++||+||||
T Consensus       163 Pa~~PnlL~NG~~GIAvGmaTnIPpHNl~Ev~~a~i~~i~np~~t~~eL~~~i~GPDFPTGg~Ii~g~~~i~~ay~tGrG  242 (745)
T PRK05561        163 PARFPNLLLNGATGIAVGMATDIPPHNLREVIDAAIHLIDNPDATLEELMEFVPGPDFPTGGEIITGRDGIRKAYETGRG  242 (745)
T ss_pred             CCCCCHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCEEEECHHHHHHHHHHCCC
T ss_conf             04687411048862487664487997669999999987449999999998318899799883897288999999984767


Q ss_pred             EEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCC-EEEEEEECCC-CCHHHHH
Q ss_conf             3899998865433678459999246443528999999999987166501445873037465-5799994798-8778999
Q gi|254780182|r  247 SIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQG-YRVVIELKRG-ASADVIL  324 (910)
Q Consensus       247 ~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~g-iRivielKr~-~~~~~vl  324 (910)
                      ||+|||||++|+.++|+++||||||||||||++|||+||+||++|||+||+||||||||+| +|||||||++ +||++||
T Consensus       243 ~i~iRak~~iE~~~~g~~~IvItEIPY~vnk~~liekIa~lv~~kki~gI~dvrDESdr~g~iRIVIelK~~~~d~~~vl  322 (745)
T PRK05561        243 SIRVRARWEIEDLARGQWQIVITELPYQVSKAKLIEQIAEQMQAKKLPGIADVRDESDRENPVRIVIEPKSNRVDPEALM  322 (745)
T ss_pred             EEEEEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCEEEEEEECCCCCCHHHHH
T ss_conf             09998899999637984179999678768489999999999970866410241036678787799999788887999999


Q ss_pred             HHHHHHCCHHCCCCCEEEEEE-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999976101100000024554-1663000299999999999999999999999999988877899999987406999999
Q gi|254780182|r  325 NQLYRYTSLQSLFSVNMVALN-GYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRI  403 (910)
Q Consensus       325 n~Lyk~T~Lq~sf~~N~~aL~-~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~i  403 (910)
                      |+|||||+||+||++||+||+ ||+|++|||+++|++|++||++||+||++|+|+||++|+||||||++|++|||+||+|
T Consensus       323 n~Lyk~T~Lq~sf~~N~~al~~dg~P~~l~Lk~iL~~~l~hR~~vi~rrt~~~L~Ka~~RlhIleGLliA~~~iD~VI~i  402 (745)
T PRK05561        323 NHLFATTDLESSYRVNMNVIGLDGRPRVKGLKEILSEWLDHRREVVTRRSQFRLDKVEKRLHILEGLLIAFLNIDEVIEI  402 (745)
T ss_pred             HHHHHHCCCHHHCCCEEEEEECCCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH
T ss_conf             99998576242137148999379975582799999999999999999999999999999999998899999676899999


Q ss_pred             HHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             86189978987877631269788999997402211122234452369999999998789999888799999989999999
Q gi|254780182|r  404 IRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIE  483 (910)
Q Consensus       404 IR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~  483 (910)
                      ||+|+   +||.+||++                          |+|||.||+|||+|||||||+||+++|++|+++|.++
T Consensus       403 IR~S~---dak~~L~~~--------------------------f~lse~QA~AIL~mrL~rLt~LE~~kl~~E~~eL~~~  453 (745)
T PRK05561        403 IRESD---EPKANLMAR--------------------------FGLTEIQAEAILELRLRRLAKLEEIEIRKEQDELRKE  453 (745)
T ss_pred             HHCCC---HHHHHHHHH--------------------------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             97063---266777555--------------------------0879999999999999998766799999999999999


Q ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCC--CCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCC
Q ss_conf             998875304989999999998999998405688331001343--453010145678189990797052331000002334
Q gi|254780182|r  484 IKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLL--DMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRR  561 (910)
Q Consensus       484 I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~--~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~R  561 (910)
                      |++|++||+|+++++++|++||.+++++|||||||+|.++..  +++.||+|++|+|+|++|+.|||||++...+.    
T Consensus       454 I~~l~~IL~s~~~~~~iI~~EL~eik~kfgd~RRT~I~~~~~~~~i~~edlI~~E~v~V~lS~~GyIKr~k~~~~~----  529 (745)
T PRK05561        454 IAELEAILASERKLWKLIKKELKADAKKFGDPRRTPIEEREEAKAIDEEALVPDEPVTVVLSKKGWVRRAKGHDID----  529 (745)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCEEEECCCEEEEEECCCCCC----
T ss_conf             9999999638999999999999999986389986302267420237877717676618998178049984488867----


Q ss_pred             CCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCC
Q ss_conf             56521100014641010113323777399995489399982000432244456554124545365562002566301256
Q gi|254780182|r  562 GGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDES  641 (910)
Q Consensus       562 ggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~  641 (910)
                          .+++++|++|++.++++|+|||+||||||.||+||+++|+||  +++++|+||.|+++++++|+|++++++++   
T Consensus       530 ----~~~~~~Ke~D~v~~~~~~~T~d~LLfFTn~Grvy~lkv~~IP--~~r~~G~pi~nll~L~~~EkIv~vl~~~~---  600 (745)
T PRK05561        530 ----PAGLGYKEGDSLLFAFEARTTDKLLFFTSTGRVYSLPVHELP--SARGQGEPLTGLIDLEPGEEIVHVLVGDP---  600 (745)
T ss_pred             ----CCCCCCCCCCCEEEEEEEECCCEEEEEECCCEEEEEEHHHCC--CCCCCCCCHHHCCCCCCCCEEEEEEEECC---
T ss_conf             ----544567778532589998069769999579759998922087--86678808988068999996999998589---


Q ss_pred             CCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCC-CCEEEEEECCCEEEEEEHHHCCCCCCCC
Q ss_conf             668717999947991898423686204777227866158985788896189-8269999369859997587623547866
Q gi|254780182|r  642 SWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQ-ENDILLTTKLGQCVRFPISAIRVFAGRN  720 (910)
Q Consensus       642 ~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~-~~~Iil~T~~G~~lrF~~~evr~~~GR~  720 (910)
                         +.+|+|+|++|++||+++++|.+.+++|++||+|++||++++|..+++ +++|+++|++|+++||+++++|+| || 
T Consensus       601 ---~~~lllaTk~G~~kr~~l~e~~~~~k~G~~ai~L~~gDelv~~~~i~~~~d~I~lvT~~Gk~lrF~~~evr~~-gR-  675 (745)
T PRK05561        601 ---DQKLLLASSAGYGFVVSEEDLVGRNRAGKAVINLKDGDKVLAPVPVEGDEDSLAAITQRGRLLVFPLSELPEL-SR-  675 (745)
T ss_pred             ---CCEEEEEECCCEEEEEEHHHHCCCCCCCEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCEEEEEHHHCCCC-CC-
T ss_conf             ---8769999789329997869800446267188861899889888994699988999958982899798887775-75-


Q ss_pred             CCCEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEE
Q ss_conf             55357675289986999897336665420000012223333333455544444444333222223200111012568679
Q gi|254780182|r  721 SVGVRGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFI  800 (910)
Q Consensus       721 a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~I  800 (910)
                      ++||+||+|+++|.|+++.+++..+.                                                   -.+
T Consensus       676 gkGVkgikLk~~D~Vv~~~vv~~~~~---------------------------------------------------l~v  704 (745)
T PRK05561        676 GKGVKLIELKKEEGLADLAVLPPGDG---------------------------------------------------LTL  704 (745)
T ss_pred             CCCCCEEEECCCCEEEEEEEECCCCC---------------------------------------------------EEE
T ss_conf             46801476689998999999858883---------------------------------------------------499


Q ss_pred             EEEECCCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEE
Q ss_conf             999759934530178848667577414887606777768689
Q gi|254780182|r  801 LTVSEKGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALV  842 (910)
Q Consensus       801 L~vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv  842 (910)
                      ++.+++|+||+|++++|+. +|||+|++..+..++  +|++.
T Consensus       705 ~s~~~~g~~k~t~l~~y~~-~Rgg~G~~~~k~~~k--~gk~~  743 (745)
T PRK05561        705 HAGKRKLTLKPKDLEEYRG-KRARRGSLLPRGLQR--VDRLS  743 (745)
T ss_pred             EECCCCCCCCCCCHHHHCC-CCCCCCCCCCCCCCC--CCCCC
T ss_conf             9867876345551677462-247788678888887--89717


No 5  
>COG0188 GyrA Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=2119.48  Aligned_cols=794  Identities=55%  Similarity=0.893  Sum_probs=775.5

Q ss_pred             EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             66600999998767877799886313754000897367899999998789999981134042556643668870478999
Q gi|254780182|r   16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD   95 (910)
Q Consensus        16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~   95 (910)
                      |.+++|+++|++|||+||||||++||||||||||||||||||||||++|++||+||+||||+|||||||||||||+||||
T Consensus         8 i~~v~i~~e~~~syl~YAmsVIv~RALPdVRDGLKPVqRRILYaM~e~gl~~d~~~kKsAriVGdvmGkyHPHGDssiYd   87 (804)
T COG0188           8 IEPIDIEDEMKRSYLDYAMSVIVGRALPDVRDGLKPVQRRILYAMFELGLTPDKKYKKSARIVGDVMGKYHPHGDSSIYD   87 (804)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             51265999999999988799886401775234786089998899997499989970003066775335678887168999


Q ss_pred             HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCH
Q ss_conf             99971220111561314788708877697201357899978999999863076840533068988548503432273211
Q gi|254780182|r   96 ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVL  175 (910)
Q Consensus        96 a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL  175 (910)
                      ||||||||||||||||||||||||+||||||||||||||||++|++||.||+++||||+|||||+++||+||||+|||||
T Consensus        88 alVRMAQdfs~RypLVdgqGNFGSiDgD~aAAMRYTEaRLs~ia~elL~di~kdtVdf~~NyDg~~~EP~VLPa~~PnLL  167 (804)
T COG0188          88 ALVRMAQDFSLRYPLVDGQGNFGSIDGDPAAAMRYTEARLSKIAEELLEDIDKDTVDFVPNYDGSEKEPEVLPARFPNLL  167 (804)
T ss_pred             HHHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHHHHHHHCHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCCCCCCEEE
T ss_conf             99997104341576231687788999973787778886231989998744465705144079998558740346687067


Q ss_pred             HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEE
Q ss_conf             01676101013317898547899999988761877688888863458668874434475889999870120389999886
Q gi|254780182|r  176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSH  255 (910)
Q Consensus       176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~  255 (910)
                      +|||+|||||||||||||||+||||||+++|+||++++++||++||||||||||+|+|.+||++||+||||+|++||+|+
T Consensus       168 vNGssGIAVGmATnIPPHNl~Ev~da~~~li~np~~~~~~lm~~i~GPDFPTgg~I~g~~~I~~aY~tGrG~i~vRa~~~  247 (804)
T COG0188         168 VNGSSGIAVGMATNIPPHNLGEVIDALIALIDNPDATIDELMEIIKGPDFPTGGIIIGRSGIREAYETGRGSIRVRAKAE  247 (804)
T ss_pred             ECCCCCEECCEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCEEECCHHHHHHHCCCCCEEEEEEEEE
T ss_conf             60687410123057799898999999999970999746777310699989986668541456787700784599998999


Q ss_pred             EEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHC
Q ss_conf             54336784599992464435289999999999871665014458730374655799994798877899999997610110
Q gi|254780182|r  256 IEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQS  335 (910)
Q Consensus       256 ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~  335 (910)
                      +|+.++||++||||||||||||++|||+||+++++||+.||+++||||||+|+|||||+||++.+++|||+|||+|+||+
T Consensus       248 iE~~~~gr~~IvItEiPyqvnka~lie~Iaelv~~kki~gis~vrDEsdr~giRivIelk~~~~~~~vln~Lfk~T~LQ~  327 (804)
T COG0188         248 IEDTKNGREQIVITEIPYQVNKAKLIEKIAELVKEKKIEGISDIRDESDREGIRIVIELKRDAVAEVVLNNLFKLTDLQT  327 (804)
T ss_pred             EEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHCHHHH
T ss_conf             99537883389999669701589999999999854873573000010268870799997776417899999987441877


Q ss_pred             CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Q ss_conf             00000245541663000299999999999999999999999999988877899999987406999999861899789878
Q gi|254780182|r  336 LFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARR  415 (910)
Q Consensus       336 sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~  415 (910)
                      +|++||+||++|+|++|+|++||++|++||++|++||++|+|+||++|+||||||++|++|||+||+|||+|+++.+||.
T Consensus       328 ~f~~nm~ai~~~~P~~~~L~~iL~~~~~hr~~vi~rR~~~~L~Ka~~R~hileGl~~a~~~iDevI~iIr~s~~~~~a~~  407 (804)
T COG0188         328 SFNVNMLALVNGRPKVLNLKEILSEFLEHRLEVVTRRTEYELNKAEERLHILEGLLIALLNIDEVIEIIRESKDKPEAKE  407 (804)
T ss_pred             HHCCEEEEECCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             50710687317803153799999999999999988999999999999998998899999714788988870898167899


Q ss_pred             HHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             77631269788999997402211122234452369999999998789999888799999989999999998875304989
Q gi|254780182|r  416 ELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRS  495 (910)
Q Consensus       416 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~  495 (910)
                      .||++                          |.||+.||+|||+|||||||+||++++++|+++|.++|++|++||+|++
T Consensus       408 ~L~~~--------------------------f~lse~Qa~aIl~mrL~rLt~le~~~i~~E~~~L~~~i~~l~~iL~s~~  461 (804)
T COG0188         408 ELMAR--------------------------FGLSEKQAEAILDLRLRRLTGLEEEKIEKELKELEKEIADLEKILASEE  461 (804)
T ss_pred             HHHHH--------------------------CCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             99987--------------------------3896788999986267776404087888899999999999998753889


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEECCCC-CCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999999998999998405688331001343-4530101456781899907970523310000023345652110001464
Q gi|254780182|r  496 RLLGIIKQELLSVKDELDTPRRTRIVEGLL-DMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDE  574 (910)
Q Consensus       496 ~l~~iI~~EL~eik~kygd~RRT~I~~~~~-~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~  574 (910)
                      ++++++++||.+++++||++|||+|..... +++.||+|++|+++|++|+.||+||++++.|++|+     +.++.+|++
T Consensus       462 ~~~~~i~~eL~~~~~k~gd~Rrt~i~~~~~~~~~~edli~~e~vvv~ls~~gyikr~~~~~~~~q~-----~~~~~~ke~  536 (804)
T COG0188         462 RLLDIIKKELLEIKKKFGDERRTEIVEEEEDEIEDEDLIAEEDVVVTLSHKGYIKRVPLKGYEAQR-----VSGLGLKEG  536 (804)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEHHCCCCCCCCCHHHHCCCCCEEEEECCCCEEEECCHHHHHHHH-----HHHCCCCCC
T ss_conf             999999999999998718532000115653223213313355449998165327863456643302-----211132434


Q ss_pred             CHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECC
Q ss_conf             10101133237773999954893999820004322444565541245453655620025663012566687179999479
Q gi|254780182|r  575 DFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKH  654 (910)
Q Consensus       575 D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~  654 (910)
                      |++...++|+|||++|||||.|++|++++|++|+++|+++|+|+.|+++++++|+|+++++++      ++.|++|+|++
T Consensus       537 d~~~~~~~~~t~d~ll~ft~~G~~y~~~~~~lp~~~~~~~G~~i~~ll~~~~~E~i~~v~~~~------~~~~l~~~T~~  610 (804)
T COG0188         537 DFLERLFEANTHDTLLFFTSKGRVYKLKVYELPEGSRRSRGEPIVNLLSLEKGEKITAVLPVN------DDQYLFLATKK  610 (804)
T ss_pred             CHHHHEEEECCCCEEEEECCCCCEEEECCEECCCCCCCCCCHHHHHHCCCCCCCEEEEEEECC------CCEEEEEEECC
T ss_conf             033430550466469998278848973130335556666781035424578885479999707------86059999169


Q ss_pred             CCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECC-CCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCC
Q ss_conf             9189842368620477722786615898578889618-982699993698599975876235478665535767528998
Q gi|254780182|r  655 GNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCT-QENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGD  733 (910)
Q Consensus       655 G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~-~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D  733 (910)
                      |++||+++++|.+.+++|+++|+|+++|+++++..+. ++++++++|++|+++||+.+++|+| ||+|+||+||+|+++|
T Consensus       611 G~vK~~~l~~f~~~~~~g~~ai~L~~~d~l~~~~~~~~~~~~i~~~t~~G~~~~F~~~~v~~~-gr~a~Gv~~i~l~~~d  689 (804)
T COG0188         611 GYVKKTSLSEFKNIRSKGKIAIKLKEGDELVSVSLTSDGDDDILLVTSNGKALRFPESEVREM-GRGAKGVKGIKLKEGD  689 (804)
T ss_pred             CCEEEEEHHHHHCCCCCCEEEEECCCCCCEEEEEECCCCCCEEEEEECCCEEEEEEHHHCCCC-CCCCCCCCEEECCCCC
T ss_conf             947982035531235677068971777630124521578760899914873787403442211-5413686406437657


Q ss_pred             EEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEE
Q ss_conf             69998973366654200000122233333334555444444443332222232001110125686799997599345301
Q gi|254780182|r  734 QVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEKGFGKRTS  813 (910)
Q Consensus       734 ~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~  813 (910)
                      .++++.++.+..                                                    .++|++|++|||||++
T Consensus       690 ~~~~~~~~~~~~----------------------------------------------------~~~l~~t~~g~~kr~~  717 (804)
T COG0188         690 KVVSLSVVEDDE----------------------------------------------------AKLLTVTERGYGKRTK  717 (804)
T ss_pred             EEEEEEECCCCC----------------------------------------------------EEEEEEECCCCEEECC
T ss_conf             566532014786----------------------------------------------------0589984367200041


Q ss_pred             HHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCCCEEEE
Q ss_conf             78848667577414887606777768689999728996499994599899999010554451568738898089987999
Q gi|254780182|r  814 SYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKDERVVS  893 (910)
Q Consensus       814 ~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~D~Vv~  893 (910)
                      +.+|+.++||++|++.++.++++ +|.++++..+.++|++|++|+.|+++|+++++|+.+||+|+||+++++.++++|++
T Consensus       718 ~~~~~~~~Rg~~G~~~~~~~~~~-~~~~~~~~~v~~~~~~~~~t~~g~~ir~~~~~i~~~~r~t~gv~~~~~~~~~~v~~  796 (804)
T COG0188         718 ISEYPVTKRGGKGVILIKGTKRN-RGKVVAAITVDEDDEIMLITSRGKLIRTAVSEISITGRNTQGVKLINLDEDEKVVS  796 (804)
T ss_pred             HHHCCCCCCCCCCEECCCCCCCC-CCEEEEEECCCCCCEEEEECCCCEEEEEECCCCCCCCCCCCCEEEEECCCCCEEEE
T ss_conf             42134246676641245455565-53377641368875389982696389853143231244456627653179973788


Q ss_pred             EEEECCC
Q ss_conf             9983566
Q gi|254780182|r  894 VERIRES  900 (910)
Q Consensus       894 va~i~~~  900 (910)
                      ++++.++
T Consensus       797 ~~~~~~~  803 (804)
T COG0188         797 VARVKEE  803 (804)
T ss_pred             EEECCCC
T ss_conf             7740578


No 6  
>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=1906.90  Aligned_cols=729  Identities=38%  Similarity=0.635  Sum_probs=706.1

Q ss_pred             EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             66600999998767877799886313754000897367899999998789999981134042556643668870478999
Q gi|254780182|r   16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD   95 (910)
Q Consensus        16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~   95 (910)
                      +.+.+|++.|..||-.||.|+|++|||||+|||||||||||||||+++|++||+|||||||.||+|||||||||||||||
T Consensus         1 ~~~~~Le~v~g~~F~kYaKYIIQDRALPD~RDGLKPVQRRILYaM~~~G~~fdk~YkKSAr~VGev~GkYHPHGDSSiYd   80 (745)
T TIGR01061         1 IINLPLEEVVGESFGKYAKYIIQDRALPDIRDGLKPVQRRILYAMSEDGNTFDKPYKKSARTVGEVIGKYHPHGDSSIYD   80 (745)
T ss_pred             CCCCCHHHHHHCCCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHH
T ss_conf             97875035440000000251340456665111577035778766532378668870012011102226712898644778


Q ss_pred             HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCH
Q ss_conf             99971220111561314788708877697201357899978999999863076840533068988548503432273211
Q gi|254780182|r   96 ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVL  175 (910)
Q Consensus        96 a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL  175 (910)
                      |||||+|+|.+|..||+.|||-||+||||||||||||||||++|.+||+||||+||.|+||||+|++||+||||.|||||
T Consensus        81 AmvRMSQ~WKn~~~lv~mHGNnGSiDGDnaAAMRYTEaRLS~iA~~LL~di~K~~V~F~~NFDDseKEP~vLP~lfPNLL  160 (745)
T TIGR01061        81 AMVRMSQDWKNNLVLVEMHGNNGSIDGDNAAAMRYTEARLSKIASELLKDIDKKTVKFIPNFDDSEKEPTVLPALFPNLL  160 (745)
T ss_pred             HHHHCCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             86414746334318998506667889985155432476677999999740477831033687788877742344213456


Q ss_pred             HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEE
Q ss_conf             01676101013317898547899999988761877688888863458668874434475889999870120389999886
Q gi|254780182|r  176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSH  255 (910)
Q Consensus       176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~  255 (910)
                      ||||||||.||||||||||++||+||+|+.||+|+|++++||+++|||||||||+|++.+||++||+||+|+|.|||+++
T Consensus       161 iNGatGIaAGYATnIpPHn~~Ev~Da~i~rId~P~c~v~~L~e~~kgPDFPTGG~i~~~~~~~~aY~tGkGk~iirak~~  240 (745)
T TIGR01061       161 INGATGIAAGYATNIPPHNLNEVIDALIYRIDHPDCSVDKLMEIVKGPDFPTGGIIQGEDGIKKAYETGKGKFIIRAKIE  240 (745)
T ss_pred             HHHHHHHHCCHHCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCEEECHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             52013320000047788876689999986138988417889854484115887246141547889854981399986425


Q ss_pred             EEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHC
Q ss_conf             54336784599992464435289999999999871665014458730374655799994798877899999997610110
Q gi|254780182|r  256 IEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQS  335 (910)
Q Consensus       256 ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~  335 (910)
                      +|..++|++|||||||||.||||.||.+|.|..-++|+.||+.|||||||+|+||+||+|++++++.|||+|||+|+||.
T Consensus       241 ~e~~~ng~~QI~It~IPYE~nKAnlvK~iedi~~d~kv~gi~eVrDeSDr~GlriiI~~Kk~~~~e~v~nyLyK~T~Lqi  320 (745)
T TIGR01061       241 IEVNKNGLNQIVITEIPYETNKANLVKKIEDIIVDKKVAGIEEVRDESDRKGLRIIIELKKDANAEKVLNYLYKKTDLQI  320 (745)
T ss_pred             EEEECCCCCEEEECCCCHHHHHHHHEEEEEEEEECCEEHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHCCCCCCEE
T ss_conf             53205882048974574677667640000026764500000100344575755465605452475567875413435438


Q ss_pred             CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Q ss_conf             00000245541663000299999999999999999999999999988877899999987406999999861899789878
Q gi|254780182|r  336 LFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARR  415 (910)
Q Consensus       336 sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~  415 (910)
                      ||++||+||++..|.++||..+|++|+.|++|||.+|..|+|+||+.|+||+|||++|++-|||||++||+|.|+.|||+
T Consensus       321 ~YN~n~vaI~nr~P~lv~L~~yLd~yi~h~~evi~~~~~Ydl~ka~~R~~IveGLik~isilDeiI~~IRas~~k~DAk~  400 (745)
T TIGR01061       321 NYNFNMVAIANRTPILVGLLSYLDAYIKHSKEVIINRSLYDLEKAKKRLEIVEGLIKAISILDEIIKLIRASEDKSDAKE  400 (745)
T ss_pred             EECCCCEEECCCCCEEECHHHHHHHHHHHHHHHEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
T ss_conf             64324178404763364401688888723023200246423888987889888899999998789887730245336034


Q ss_pred             HHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             77631269788999997402211122234452369999999998789999888799999989999999998875304989
Q gi|254780182|r  416 ELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRS  495 (910)
Q Consensus       416 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~  495 (910)
                      +|+..                          |.||+.|||||..|||||||+.++-.|++|.+||.++|+.|+.+|+|++
T Consensus       401 ~Li~~--------------------------f~FT~~QAEAIv~LrLY~LTnTDi~~L~~E~~eL~~~~~~l~~~i~~~k  454 (745)
T TIGR01061       401 NLIDK--------------------------FEFTENQAEAIVSLRLYRLTNTDIFELKEEEEELEKKIKSLEEIIASEK  454 (745)
T ss_pred             HHCCC--------------------------CCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             31011--------------------------3777257999999886037320377778789999999999999876578


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEECCCC--CCCCCCCCCCCCEEEEEECCC-EECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999999998999998405688331001343--453010145678189990797-05233100000233456521100014
Q gi|254780182|r  496 RLLGIIKQELLSVKDELDTPRRTRIVEGLL--DMEDEDCIVREDMVVTVSHLG-YVKRVPLSVYRAQRRGGKGRSGVVMR  572 (910)
Q Consensus       496 ~l~~iI~~EL~eik~kygd~RRT~I~~~~~--~i~~EdlI~~E~vvV~lS~~G-yIKr~~~~~yr~Q~RggkG~~~~~~k  572 (910)
                      .+.++|+++|.++||+|+++|||.|.+...  +++.+.||+++++-|++|+.| |+||++..+|.+.+     ...++.+
T Consensus       455 ~~~~~lk~~l~~~KK~F~~~R~s~l~~~~~~~~i~~~~li~~~~~~v~itk~GnY~K~~S~~sf~ss~-----~~d~g~~  529 (745)
T TIGR01061       455 ARKKLLKKKLKELKKKFAQERRSKLEDEIEKIKINEDELIEKEDLYVVITKDGNYIKRTSKRSFASSK-----YDDFGLK  529 (745)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHEECCHHHHHHHCCCEEEEEECCCEEHHHHHHHHHHCC-----CCCCCCC
T ss_conf             99999899999872310575045675116530104678532146407998447630001266762047-----3115775


Q ss_pred             CCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEEEE
Q ss_conf             641010113323777399995489399982000432244456554124545-3655620025663012566687179999
Q gi|254780182|r  573 DEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILS-LNQGERITTIMPFPEDESSWNNLYVVFA  651 (910)
Q Consensus       573 e~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lvl~  651 (910)
                      ++|-+.+...++|||.||+|||.|++..++||+||..+|+.-|.|++|.+. +..+|+|+.+.++++|+  .+..+|||+
T Consensus       530 ~~d~l~~~~~~nttd~lL~~Ts~g~~In~pvh~La~~rwkd~g~hls~~~~n~~~~E~iv~v~~~~~fd--v~~~~L~l~  607 (745)
T TIGR01061       530 DDDILFYQTIANTTDKLLIFTSKGNLINLPVHKLADIRWKDLGEHLSNKITNFDENETIVAVEILNEFD--VDEAILVLA  607 (745)
T ss_pred             CCHHHHHHHHHHCCCEEEEEECCCCEEEEEEEECCCCCHHHHHHHHCCHHHHHHCCCCEEEEEEECCCC--CCHHHHHHH
T ss_conf             533453546521225378876166664213031456656689987200011021068489998613225--746898998


Q ss_pred             ECCCCEEEECHHHHHHCC---CCCEEEEEECCCCEEEEEEECCC--CCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEE
Q ss_conf             479918984236862047---77227866158985788896189--8269999369859997587623547866553576
Q gi|254780182|r  652 TKHGNVRRNKLSDFIQIN---RSGKIAMKLDSRDEILSVETCTQ--ENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRG  726 (910)
Q Consensus       652 Tk~G~VKkt~l~ef~~~r---~~G~~aikLkegD~Li~v~~~~~--~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkg  726 (910)
                      |+.|+|||+.+++|.-.+   +..+.+++|+++|.||+|++..+  ++.|+++|+.|++|+|.++||+.+ |+.|+||||
T Consensus       608 sklg~vKriel~~l~~~~~y~sK~~~~~~L~D~d~li~a~~~~~Gh~~~i~lvS~~gy~l~F~~~Ei~~~-~~~A~GvK~  686 (745)
T TIGR01061       608 SKLGMVKRIELTELDIKRNYRSKAILILKLKDEDELISAFLQKKGHDKLIILVSKLGYALLFLVEEINVV-GAKAAGVKG  686 (745)
T ss_pred             HHCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEEEEECCCEEEECCEEECCC-CCCCCCEEE
T ss_conf             7558747876032477865101223321117895438999841888441899973683577302033231-446673113


Q ss_pred             EECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECC
Q ss_conf             75289986999897336665420000012223333333455544444444333222223200111012568679999759
Q gi|254780182|r  727 ISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEK  806 (910)
Q Consensus       727 IkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~  806 (910)
                      |+|+++|.|.+..+....+                                                     ++..+|..
T Consensus       687 mkLK~~D~v~~~~i~~~~~-----------------------------------------------------~~vll~~~  713 (745)
T TIGR01061       687 MKLKEDDEVKSGLILEANE-----------------------------------------------------SLVLLTQR  713 (745)
T ss_pred             EECCCCCEEEEEEEECCCC-----------------------------------------------------CEEEEEEC
T ss_conf             3057676389999982799-----------------------------------------------------55899736


Q ss_pred             CCEEEEEHHHCCCCCCCCCCEEEEE
Q ss_conf             9345301788486675774148876
Q gi|254780182|r  807 GFGKRTSSYDFRISNRSGKGIRATD  831 (910)
Q Consensus       807 G~GKRt~~~eyr~q~RGgkGv~~ik  831 (910)
                      |-.||.+++|+..++|+..|+..++
T Consensus       714 Gs~k~~~~~El~~~sRa~~~~~llR  738 (745)
T TIGR01061       714 GSVKRLSISELKVTSRAATGVKLLR  738 (745)
T ss_pred             CCEEEEEHHHHHHHHHHCCCCHHHC
T ss_conf             8256510365555343116511110


No 7  
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit; InterPro: IPR005742   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=1568.00  Aligned_cols=683  Identities=36%  Similarity=0.598  Sum_probs=641.7

Q ss_pred             EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH
Q ss_conf             66600999998767877799886313754000897367899999998789999981134042556643668870478999
Q gi|254780182|r   16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD   95 (910)
Q Consensus        16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~   95 (910)
                      |..+++.+..+++||.||||||++|||||||||||||||||+|||.+|||.++..||||||+||||+||||||||+||||
T Consensus         1 iE~~~l~~~~~~~YL~Y~~~~IM~RaLP~i~DGLKPV~RR~~YAM~~L~L~a~a~yKKsAR~VGDVlGKyHPHGD~A~Y~   80 (747)
T TIGR01062         1 IENLDLRNFTEEAYLNYSLYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNANAKYKKSARTVGDVLGKYHPHGDSAVYE   80 (747)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEECCEECCCCCCCCCCCCHHHHH
T ss_conf             97651578988888888888887423772025775146899888887164767775200102102124605896248999


Q ss_pred             HHHHHCCCHHCCCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCC
Q ss_conf             999712201115613147887088776-9720135789997899999986307684053306898854850343227321
Q gi|254780182|r   96 ALARMAQDWSLRLLLIEGQGNFGSVDG-DPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNV  174 (910)
Q Consensus        96 a~v~maq~~~~r~plidg~GnfGs~dg-d~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~l  174 (910)
                      |||+|||+||+|||||||||||||+|+ |++|||||||+|||++++-||.||+++||||+||||||..||.+|||+||||
T Consensus        81 ~~V~~AQ~FS~RYPLvDGQGN~Ga~DdP~~~AAMRYTESRl~~~s~lLl~~l~~~TvD~~~~fD~~~~EP~~lPA~lP~~  160 (747)
T TIGR01062        81 ALVLLAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKISELLLEELGQGTVDFRPNFDGTLLEPKILPARLPNI  160 (747)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             99986211123476201677868898742123433246678999999998618872133457887424644253112055


Q ss_pred             HHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCC-CHHHHHHHHHHCCCEEEEEEE
Q ss_conf             1016761010133178985478999999887618776888888634586688744344-758899998701203899998
Q gi|254780182|r  175 LVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVIL-GRTGIKNAYATGRGSIVIRGV  253 (910)
Q Consensus       175 L~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~-~~~~i~~~y~tGrG~i~iR~k  253 (910)
                      |+||++|||||||||||||||.|||||+++|||||.++++++|++|+||||||+|+|+ ..+.|+.+|++|||||++||.
T Consensus       161 L~NG~~GIAVGMAT~IPPHNl~E~adA~~~LiD~P~agl~d~l~~v~GPDfPT~a~II~~~~~I~~~Y~~GRGS~r~Ra~  240 (747)
T TIGR01062       161 LLNGTTGIAVGMATDIPPHNLRELADAALYLIDNPKAGLDDILNIVQGPDFPTEAEIIDKKEEIRKIYETGRGSVRMRAR  240 (747)
T ss_pred             HCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHCCCCEEEEEEE
T ss_conf             60688724752217888623799999999985288321689999734857898765747189999998569833897226


Q ss_pred             EEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCC-CCEEEEEEEC-CCCCHHHHHHHHHHHC
Q ss_conf             8654336784599992464435289999999999871665014458730374-6557999947-9887789999999761
Q gi|254780182|r  254 SHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDR-QGYRVVIELK-RGASADVILNQLYRYT  331 (910)
Q Consensus       254 ~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr-~giRivielK-r~~~~~~vln~Lyk~T  331 (910)
                      |+-|+...|-++||||+||||++++++|++||.+.++||||-|+|+|||||. +-+||||+++ +..|++.||++||+.|
T Consensus       241 W~KE~~syGty~ivi~~lP~Q~~~sk~i~QIA~~~~~KKlP~~~~iRDEsDH~~~iR~Vi~PR~~~~D~~~vM~~LF~~T  320 (747)
T TIGR01062       241 WKKEDGSYGTYQIVISALPHQISKSKVIEQIAIQLKDKKLPLISDIRDESDHENPIRVVIVPRSNRVDPDIVMEHLFATT  320 (747)
T ss_pred             EEECCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             53014666502676522775354015889999999717887024203423677856899843887768799999986542


Q ss_pred             CHHCCCCCEEEEE-ECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             0110000002455-416630002999999999999999999999999999888778999999874069999998618997
Q gi|254780182|r  332 SLQSLFSVNMVAL-NGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNP  410 (910)
Q Consensus       332 ~Lq~sf~~N~~aL-~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~  410 (910)
                      +||.+|.+||++| .|++|.++||.|||++|+.||+++|+||++|+|+|...|+|||+||.+|+.||||||+|||+-++|
T Consensus       321 ~LE~~~~~N~N~IG~~~~P~V~nlLEIL~E~L~fR~~~v~RR~~Y~L~Kv~~RL~IL~~L~i~fLN~DEvIEIIR~EDeP  400 (747)
T TIGR01062       321 DLEKSYRLNMNMIGLDNKPAVKNLLEILQEWLVFRRNTVIRRLTYRLNKVLKRLHILEGLLIAFLNIDEVIEIIREEDEP  400 (747)
T ss_pred             CHHHHEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC
T ss_conf             20011233224640698960454899999999855888787888779999989988764755202100101222379984


Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89878776312697889999974022111222344523699999999987899998887999999899999999988753
Q gi|254780182|r  411 ETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDI  490 (910)
Q Consensus       411 ~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~I  490 (910)
                         |..||+|                          |+||+.||+|||++|||.|.+||+.+|..|+.+|.++...|++|
T Consensus       401 ---K~~lM~R--------------------------F~ls~~Q~e~IL~~rLR~L~KLEE~~i~~E~~~L~K~~~~L~~I  451 (747)
T TIGR01062       401 ---KTILMER--------------------------FKLSEIQAEAILNLRLRHLAKLEEHKIKDEQSELEKERAILEKI  451 (747)
T ss_pred             ---HHHHHHH--------------------------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ---2899855--------------------------06358999999865555654577888876566778999999999


Q ss_pred             HCCHHHHHHHHHHHHHHHHHHCCC-----CCCCEEECCCC--CCCCC-CCCCCCCEEEEEECCCEECCCCCCCCCCCCCC
Q ss_conf             049899999999989999984056-----88331001343--45301-01456781899907970523310000023345
Q gi|254780182|r  491 LSSRSRLLGIIKQELLSVKDELDT-----PRRTRIVEGLL--DMEDE-DCIVREDMVVTVSHLGYVKRVPLSVYRAQRRG  562 (910)
Q Consensus       491 L~s~~~l~~iI~~EL~eik~kygd-----~RRT~I~~~~~--~i~~E-dlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~Rg  562 (910)
                      |+|++++|+++|+|+++..++||+     +|||.+.+-+.  .+.+. |+++.|||+|++|+.|||+..+-++-      
T Consensus       452 L~~~~~l~~l~KKEi~~~~~~yg~ntiiG~R~~~l~E~~~~~~~~~~t~~~~~EPvTii~S~MGWVRs~KGH~~------  525 (747)
T TIGR01062       452 LKSERKLNQLVKKEIQADAKKYGLNTIIGARRSSLEEREEAKQVSEITDMIPKEPVTIILSKMGWVRSAKGHDI------  525 (747)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEECCCCCC------
T ss_conf             87568999999899999998740242203554513567888888766530367881799827773550466566------


Q ss_pred             CCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCC-CCEEEEEEECCCCC
Q ss_conf             65211000146410101133237773999954893999820004322444565541245453655-62002566301256
Q gi|254780182|r  563 GKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQG-ERITTIMPFPEDES  641 (910)
Q Consensus       563 gkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~-E~I~ail~~~~~~~  641 (910)
                        ...++++|+||.....+.+.|+|.++|++|+||.|.+.+..||.+  ++.|.|+.-=|.++.| ..|..++-.+    
T Consensus       526 --D~~~l~YK~GD~~~~~~~~~~~~~v~~i~S~GR~y~l~~~~l~~a--~g~G~Pl~~KL~l~~Gn~~i~~~l~~~----  597 (747)
T TIGR01062       526 --DLSTLKYKAGDSEKAIIEGKSNQKVVFIDSTGRSYALDPLNLPSA--RGQGEPLTGKLLLPIGNATIENILMES----  597 (747)
T ss_pred             --CCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEEECCCCCCCC--CCCCCCEEEEEECCCCCCCEEEEEEEC----
T ss_conf             --714354136861233455127751799972885266311204345--677872268873268862310777635----


Q ss_pred             CCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCC-EEEEEECCCEEEEEEHHHCCCCCCCC
Q ss_conf             66871799994799189842368620477722786615898578889618982-69999369859997587623547866
Q gi|254780182|r  642 SWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQEN-DILLTTKLGQCVRFPISAIRVFAGRN  720 (910)
Q Consensus       642 ~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~-~Iil~T~~G~~lrF~~~evr~~~GR~  720 (910)
                        +++.|+|++.-|+.+-...+++...++.|+..|+|-|+-+++.+..+.+++ -|+++|..|++|.|++++++.|+  +
T Consensus       598 --~~Q~LL~AS~~G~GF~~~~~~liA~~k~GK~l~~lPE~~~~~~p~~~~~~s~~~~aI~~a~R~L~F~~~~lP~l~--K  673 (747)
T TIGR01062       598 --ENQKLLLASDAGYGFLVKFNDLIARNKAGKALINLPENASVLAPLVVNDDSDLIVAITEAGRLLVFPIDDLPELS--K  673 (747)
T ss_pred             --CCCCEEEECCCCCCEEEECHHHHHHCHHCHHHCCCCCCCEEECCEEECCCCCEEEEECCCCEEEEECHHHCCCCC--C
T ss_conf             --885321000168624740043333110040200178886110443423761024441136706874211177634--7


Q ss_pred             CCCEEEEECCC------CCEEEEEEEECCCC
Q ss_conf             55357675289------98699989733666
Q gi|254780182|r  721 SVGVRGISLAK------GDQVISMAIVLHAD  745 (910)
Q Consensus       721 a~GVkgIkL~~------~D~Vv~~~vi~~~~  745 (910)
                      ++|++.++++.      .|-+....++++.+
T Consensus       674 G~G~~~~~~~~a~A~~~~~~L~~l~~~~~Q~  704 (747)
T TIGR01062       674 GKGNKLIRIPAANAKDREELLLDLKILNKQD  704 (747)
T ss_pred             CCCCEEEEECCHHHCCCCCCCEEEEEECCCC
T ss_conf             8730577505410012000101234535777


No 8  
>PRK09631 DNA topoisomerase IV subunit A; Provisional
Probab=100.00  E-value=0  Score=1402.78  Aligned_cols=609  Identities=25%  Similarity=0.421  Sum_probs=511.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf             09999987678777998863137540008973678999999987899999811340425566436688704789999997
Q gi|254780182|r   20 SITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALAR   99 (910)
Q Consensus        20 ~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~   99 (910)
                      +|+++|++|||+||||||++|||||||||||||||||||||++++   +++|+|||||||+|| |||||||+||||||||
T Consensus         2 ~i~~~~~~~~l~Ya~~VI~~RAlPdv~DGLKPvqRRiL~~m~~~~---~~~~~K~A~ivG~~m-kyHPHGd~siy~alV~   77 (626)
T PRK09631          2 DIKTLLKDNFLQYSSYVIKDRAIASVIDGFKPVQRRIIHSLFEMH---DGNFHKVANVVGNTM-KYHPHGDTSIYEALVN   77 (626)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCC---CCCCCEEEEEECCCC-CCCCCCCHHHHHHHHH
T ss_conf             868999999998889998850277521488659999999998648---999857628850511-2689982479999999


Q ss_pred             HCCCHHCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCC
Q ss_conf             122011156131478870887-7697201357899978999999863076840533068988548503432273211016
Q gi|254780182|r  100 MAQDWSLRLLLIEGQGNFGSV-DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNG  178 (910)
Q Consensus       100 maq~~~~r~plidg~GnfGs~-dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG  178 (910)
                      |||    |||||||||||||+ ||||||||||||||||++|++||  ++++||||+|||||+++||+||||+|||||+||
T Consensus        78 maq----~~~lid~qGNfGsi~~gD~aAA~RYtEaRls~~a~e~l--~~~~tv~~~~nyDg~~~EP~vLP~~~PnLL~nG  151 (626)
T PRK09631         78 IAN----KDLFIEKQGNFGNLFTGDPASASRYIECRLTPLAFEVL--YSKEITSYEPSYDGRNNEPLIFPAKIPVILIQG  151 (626)
T ss_pred             HHC----CCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH--CCCCCCEECCCCCCCCCCCEEEECCCCHHHHCC
T ss_conf             856----57605278888899998834566689897799999983--787851201278987446405553573777526


Q ss_pred             CCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEEE
Q ss_conf             76101013317898547899999988761877688888863458668874434475889999870120389999886543
Q gi|254780182|r  179 GGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIEK  258 (910)
Q Consensus       179 ~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie~  258 (910)
                      |+|||||||||||||||+|||||++++|+||++++        +|||||||+|..     +.|+||||+|++|||+++++
T Consensus       152 ~~GIAVGmaT~IpPHNl~Evida~i~~l~~~~~~~--------~PDFPTGG~i~~-----~~Y~tG~G~i~vRak~e~~~  218 (626)
T PRK09631        152 SEGIAVGMAAKILPHNFNEILEAVKSELLGESYDL--------YPDFPTGGIVDV-----NEYADGNGKVLVRAKIETTD  218 (626)
T ss_pred             CCCHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCC--------CCCCCCCCCCCH-----HHHHCCCEEEEEEEEEEECC
T ss_conf             74221222106899888999999998533898766--------999998751033-----25634862799999999817


Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCC
Q ss_conf             36784599992464435289999999999871665014458730374655799994798877899999997610110000
Q gi|254780182|r  259 TSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFS  338 (910)
Q Consensus       259 ~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~  338 (910)
                          +.+||||||||||||++|||+|++++++|||+ |+||||||+ +++||||+||||++|+++||+||++|+||+|||
T Consensus       219 ----~~~ivItEiPy~v~k~~lie~I~~~~~~~ki~-I~~i~D~s~-~~vrIvi~lk~~~~~~~vln~Ly~~T~lq~sf~  292 (626)
T PRK09631        219 ----EKTIVIRELPFGETTESLIASIEKAIRKNYIK-VSSINDFTA-ENVEIELKLPRGVYASEVIEKLYHYTNCQVSIS  292 (626)
T ss_pred             ----CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCC-CCCCCCCCC-CCEEEEEEECCCCCHHHHHHHHHHHCCHHHEEC
T ss_conf             ----83599995687777899999999999725676-211414689-827999998999998999999875097132176


Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             00245541663000299999999999999999999999999988877899999987406999999861899789878776
Q gi|254780182|r  339 VNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELM  418 (910)
Q Consensus       339 ~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~  418 (910)
                      +||+||+||+|++|||+++|++|++||++|++||++|+|+++++|+|...+..+++++  +|++.|+.+++.+++...+.
T Consensus       293 ~n~~ai~~~~P~~l~l~eiL~~~~~h~~~vl~r~le~~l~k~~er~H~~sLe~IfIe~--rIy~~Ie~~~~~e~v~~~i~  370 (626)
T PRK09631        293 VNLLLLSDRYPVIYTVTDIIKFHAEHLQKILKMELELERSKILEKIFSKTLEQIFIEK--KIYKILETISKEEDVVSIVL  370 (626)
T ss_pred             CEEEEEECCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHCCCHHHHHHHHH
T ss_conf             2689998998279879999999999999999999998899899868999999998666--68999884201688999999


Q ss_pred             HHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH
Q ss_conf             31269788999997402211122234452369999999998789999888799999989999999998875304989999
Q gi|254780182|r  419 QRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLL  498 (910)
Q Consensus       419 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~  498 (910)
                      +......                 ..-...+|+.|++|||+|||+|||++|++|.++|+++|.++|+++++.|++   +.
T Consensus       371 ~~l~pf~-----------------~~l~r~ite~d~~aLleirL~RIT~~didK~~eei~~L~~eI~eI~~~L~~---l~  430 (626)
T PRK09631        371 SELLPFK-----------------SSLSRDVTEDDVENLLKIPIRKISLFDIDKNNKDIRILNKELKSIESNIKS---IK  430 (626)
T ss_pred             HHHHHHH-----------------HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HH
T ss_conf             8777678-----------------876301579999999998998853430887999999999999999863776---89


Q ss_pred             HHHHHHHHHHHHHCCCC--CCCEEECCCCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             99999899999840568--8331001343453010145678189990797052331000002334565211000146410
Q gi|254780182|r  499 GIIKQELLSVKDELDTP--RRTRIVEGLLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDF  576 (910)
Q Consensus       499 ~iI~~EL~eik~kygd~--RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~  576 (910)
                      .++++|+.+++++||+.  |||+|                    ++++.+|+||+++++|+.|.|+|+|+.|+++|++||
T Consensus       431 ~~~I~~l~~Lk~kYG~~~~RKTEI--------------------~lfd~i~aKrVa~~n~Kly~nr~~GFiGtslKkdDf  490 (626)
T PRK09631        431 GYAINFIDKLLAKYSKEYKRKTEI--------------------SLIKSKNVREIATKNMKVYLNLETGFVGTSLIDGEF  490 (626)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEE--------------------EEECCEEEEEEECCCCEEEECCCCCEEEECCCCCCE
T ss_conf             999999999998735477725799--------------------976444369957023325665888556103567845


Q ss_pred             HEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCC-CEEEEEEECCCCCCCCCCEEEEEECCC
Q ss_conf             1011332377739999548939998200043224445655412454536556-200256630125666871799994799
Q gi|254780182|r  577 VTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGE-RITTIMPFPEDESSWNNLYVVFATKHG  655 (910)
Q Consensus       577 v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E-~I~ail~~~~~~~~~~~~~Lvl~Tk~G  655 (910)
                      +   +.|++||+|||||| |+   .++..+|+....+|+.-..+++...++. .|-.++- ++-+           +...
T Consensus       491 V---~~CSd~DdILvF~d-G~---ykV~kV~~K~Fvgk~i~~v~v~~k~d~~~tiyn~IY-rDgk-----------~g~~  551 (626)
T PRK09631        491 I---GNASYYDKILIFKD-GS---YVLKNIEDKTFIDKKNVCVLVYDINNSKEQVFSIIY-RDKL-----------DNFY  551 (626)
T ss_pred             E---EECCCCCEEEEEEC-CE---EEEEECCCCCEECCCCEEEEEEECCCCCCEEEEEEE-ECCC-----------CCCE
T ss_conf             6---73356653999989-85---999985776054688379999852787650799999-8699-----------8836


Q ss_pred             CEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEE-ECCCEEEEEEHHHCCCCCCCCCCCEEE
Q ss_conf             18984236862047772278661589857888961898269999-369859997587623547866553576
Q gi|254780182|r  656 NVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLT-TKLGQCVRFPISAIRVFAGRNSVGVRG  726 (910)
Q Consensus       656 ~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~-T~~G~~lrF~~~evr~~~GR~a~GVkg  726 (910)
                      ++||.....+..-+  .-..  ..+|.+++....-. +  +.-. .....-.-|+-+++. ..||+|+|...
T Consensus       552 yiKRF~V~~~trdK--~Y~l--~~~~s~~l~fs~n~-n--l~~~~~~k~~~~~~df~~~~-iKgr~skGn~v  615 (626)
T PRK09631        552 YVKRFKIDKFILDK--VYEF--LPENDEFLDFSLNP-E--FVPFSRSKDIVKMIEIDNFM-VKSRSSKGKRI  615 (626)
T ss_pred             EEEEEEECCEEECC--CCCC--CCCCCEEEEEEECC-C--CCCCCCCCCEEEEECHHHEE-EECCCCCCEEE
T ss_conf             89998832388425--2245--79998799999777-6--57454424514773211403-41444555176


No 9  
>PRK09630 DNA topoisomerase IV subunit A; Provisional
Probab=100.00  E-value=0  Score=1299.61  Aligned_cols=468  Identities=28%  Similarity=0.438  Sum_probs=426.7

Q ss_pred             ECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf             00999998767877799886313754000897367899999998789999981134042556643668870478999999
Q gi|254780182|r   19 VSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALA   98 (910)
Q Consensus        19 ~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v   98 (910)
                      .+|+++|++|||+||||||++|||||||||||||||||||||++++   +++|+|||||||+||| ||||||+|||||||
T Consensus         2 ~~i~~~~~~~yl~Ya~~vI~~RAlPdvrDGLKPVqRRiLy~m~~~~---~~~~~K~ArvvG~v~g-yHPHGd~siy~alv   77 (479)
T PRK09630          2 SDVSDLFKTHFMHYASYVILERAIPHILDGLKPVQRRLLWTLFRMD---DGKMHKVANIAGRTMA-LHPHGDAPIVEALV   77 (479)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCC---CCCCCEEEEEECCEEC-CCCCCHHHHHHHHH
T ss_conf             6279999999998889999851177532588609999999983068---9987134244213511-48887278999999


Q ss_pred             HHCCCHHCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHC
Q ss_conf             712201115613147887088-7769720135789997899999986307684053306898854850343227321101
Q gi|254780182|r   99 RMAQDWSLRLLLIEGQGNFGS-VDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVN  177 (910)
Q Consensus        99 ~maq~~~~r~plidg~GnfGs-~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~n  177 (910)
                      ||||    ||||||||||||| +||||||||||||||||++|.+||  ++++||||+||||||++||+||||+|||||+|
T Consensus        78 rmaq----r~~LvdgqGNfGs~~dgd~~AAmRYtE~rls~~a~~~l--~~~dtv~f~~NyDgs~~EP~vLPa~~PnLLvN  151 (479)
T PRK09630         78 VLAN----KGYLIDTQGNFGNPLTGDPHAAARYIEARLSPLAKEVL--FNTDLMTFHDSYDGREKEPDILPAKLPLLLLH  151 (479)
T ss_pred             HHHC----CCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH--CCCCCCCCCCCCCCCCCCCCEEECCCCHHHHC
T ss_conf             9856----76156467888999899804677899987589999983--55685467789899855771211457187754


Q ss_pred             CCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEE
Q ss_conf             67610101331789854789999998876187768888886345866887443447588999987012038999988654
Q gi|254780182|r  178 GGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIE  257 (910)
Q Consensus       178 G~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie  257 (910)
                      ||+|||||||||||||||+|||||++++|+||++++        ||||||||+|.+.+     |+||||+|++||+|+++
T Consensus       152 Gs~GIAVGmAT~IpPHNl~EvidA~i~~i~~~~~~~--------~PDFPTGGii~~~~-----Y~tGrG~i~vRak~~~~  218 (479)
T PRK09630        152 GVDGIAVGMTTKIFPHNFCELLEAQIAILNDQPFTL--------LPDFPSGGLMDASE-----YQDGLGSITLRASIDII  218 (479)
T ss_pred             CCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCC--------CCCCCCCCEECHHH-----HCCCCCEEEEEEEEEEE
T ss_conf             775222345525899898999999999762898775--------89999977305466-----55789818999999997


Q ss_pred             ECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCC
Q ss_conf             33678459999246443528999999999987166501445873037465579999479887789999999761011000
Q gi|254780182|r  258 KTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLF  337 (910)
Q Consensus       258 ~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf  337 (910)
                      +.    ++||||||||||||++|+++|+++++++++ +|+|+||||+ +++||||+|||+++|+.|||+|||||+||+||
T Consensus       219 ~~----k~ivItEiPy~v~k~~lie~I~~~~~~~~~-~I~~i~D~s~-~~~rivI~lkr~~~~~~vl~~Lyk~T~Lq~sf  292 (479)
T PRK09630        219 ND----KTLLIKEICPSTTTETLIRSIENAAKRGII-KIDSIQDFST-DLPHIEIKLPKGIYAKDLLPPLFEHTECQVIL  292 (479)
T ss_pred             EC----CEEEEEECCCCCCHHHHHHHHHHHHHCCCC-CCCCEEECCC-CCCEEEEECCCCCCHHHHHHHHHHCCCHHHEE
T ss_conf             14----438997068656699999999999864876-6885113357-98559984799999999999998369624122


Q ss_pred             CCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHH---HHHHHHHHHHHHHHHCCCHH
Q ss_conf             000245541663000299999999999999999999999999988877---899999---98740699999986189978
Q gi|254780182|r  338 SVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAH---VLVGLA---IAVANLDEVVRIIRFSPNPE  411 (910)
Q Consensus       338 ~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~H---ILeGL~---~Al~nIDeVI~iIR~S~d~~  411 (910)
                      |+||+||++|+|++|+|+++|++|++||.++++||+.+ +.++..|.|   +||++.   .++++||+||++||+|++.+
T Consensus       293 ~~N~~aI~~g~P~~l~l~eiL~~~~~~~~~~lrr~l~~-~~~~~~r~~~~k~Le~l~I~~~~~d~I~eiI~~i~~~~~~e  371 (479)
T PRK09630        293 TSKPTAIYQNKPVETSISEILKLHTEALQGYLKKELLI-LQDSLTREHYHKTLEYIFIKHKLYDTVREMLSKRKTKPSAS  371 (479)
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             33237888890866668999999999875543466899-98999999999888899998778999999999885389899


Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98787763126978899999740221112223445236999999999-87899998887999999899999999988753
Q gi|254780182|r  412 TARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAIL-ELRLARLTGLGRDDIRNELNSLGIEIKECLDI  490 (910)
Q Consensus       412 eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AIL-dMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~I  490 (910)
                      +|+..+++..+...                  .......+.|+.++| +|+|+|||+||++++++|+++|.++++.++++
T Consensus       372 d~~~~l~~~~~~~~------------------~~~~~~i~~q~~~~L~~l~l~kL~~Le~~k~~~El~~l~~~i~~l~~~  433 (479)
T PRK09630        372 DLHNAVLHALEPFL------------------HTLPTAPDKQATSQLASLTIKKILCFNENAYTKELAAIEKKQAAVQKD  433 (479)
T ss_pred             HHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999998765667------------------877543389999999998999875133999999999999999999999


Q ss_pred             HCCHHHHHHHHHHHHHHHHHHCCC--CCCCEEECCCCCCCCCCCCCCCCEE
Q ss_conf             049899999999989999984056--8833100134345301014567818
Q gi|254780182|r  491 LSSRSRLLGIIKQELLSVKDELDT--PRRTRIVEGLLDMEDEDCIVREDMV  539 (910)
Q Consensus       491 L~s~~~l~~iI~~EL~eik~kygd--~RRT~I~~~~~~i~~EdlI~~E~vv  539 (910)
                      |+   ++++++++||++++++|||  +|||+|.+.+.  ..+++|+.|+++
T Consensus       434 l~---~l~kiii~eL~~ikekYGd~~eRRTeI~~~~~--~~~~~~~~e~~v  479 (479)
T PRK09630        434 LS---QLKKYTVKYLKGLLERYGHLGHRKTQITKFKA--KKTSILKQQTLI  479 (479)
T ss_pred             HH---HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC--HHHHCCCHHCCC
T ss_conf             99---99999999999999985899877675602432--343024200259


No 10 
>smart00434 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC
Probab=100.00  E-value=0  Score=1187.07  Aligned_cols=439  Identities=55%  Similarity=0.851  Sum_probs=426.8

Q ss_pred             ECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf             00999998767877799886313754000897367899999998789999981134042556643668870478999999
Q gi|254780182|r   19 VSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALA   98 (910)
Q Consensus        19 ~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v   98 (910)
                      ++|+++|.++|++||||||.+|||||+|||||||||||||||++++++++++|+|||++||+|||+||||||+|+|+|||
T Consensus         1 i~i~d~~~~~~~~ys~~vi~~RaiP~~~DGLKPvqRriLy~~~~~~l~~~~~~~k~a~~~g~~~~~YHpHGd~s~~~aiv   80 (445)
T smart00434        1 IDIEDFINKEYLDYSMSVINGRAIPDVRDGLKPVQRRILYAMFKRGLTPDEPKVKSARGVGDVMGKYHPHGDSSLYDAIV   80 (445)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEHHCCCCCCCHHHHHHHHH
T ss_conf             97799998999998899876034884002787899999999997389889862788888861001788886889999999


Q ss_pred             HHCCCHHCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHC
Q ss_conf             7122011156131478870887-769720135789997899999986307684053306898854850343227321101
Q gi|254780182|r   99 RMAQDWSLRLLLIEGQGNFGSV-DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVN  177 (910)
Q Consensus        99 ~maq~~~~r~plidg~GnfGs~-dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~n  177 (910)
                      ||||+|||||||+||||||||+ |||+||||||||||||++|..||.++|++||+|+|||||+..||+|||+.|||||||
T Consensus        81 ~mAQ~fs~n~~Ll~~~GnFGs~~~G~~aAa~RYie~rLs~~~~~~~~~~d~~~~~~~~n~Dg~~~EP~~~~p~iP~lLvN  160 (445)
T smart00434       81 RMAQDFSNNYPLLDGQGNFGSRLDGDDAAAMRYTETRLSPLARELLPDIDKDTVDFVPNYDGQEIEPTVLPPIIPNLLVN  160 (445)
T ss_pred             HHHHHHHCCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCHHCCCCCCHHEEE
T ss_conf             98474340554230588867889998203367888637799999876438780755438898726751027766730030


Q ss_pred             CCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEE
Q ss_conf             67610101331789854789999998876187768888886345866887443447588999987012038999988654
Q gi|254780182|r  178 GGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIE  257 (910)
Q Consensus       178 G~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie  257 (910)
                      ||+|||||||||||||||+||++||+++|++|+++.++||.+++||||||||+|.           |+|+|++||+|++|
T Consensus       161 Gs~GIavG~sT~IPphN~~evi~a~~~~l~~~~~~~~~l~~~p~~pdF~gg~~~~-----------g~g~~~~rg~~~~~  229 (445)
T smart00434      161 GSSGIAVGMATNIPPHNLREVIDAVRRLIDNPEASIDELMMIPWGPDFPTGGEII-----------GPGSYVVRGKIEIE  229 (445)
T ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCEEEE-----------CCCEEEEEEEEEEE
T ss_conf             7874254230477887889999988766518878889996388428999816993-----------39869999999998


Q ss_pred             ECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHC-CCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCC
Q ss_conf             3367845999924644352899999999998716650144587303-746557999947988778999999976101100
Q gi|254780182|r  258 KTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDES-DRQGYRVVIELKRGASADVILNQLYRYTSLQSL  336 (910)
Q Consensus       258 ~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeS-dr~giRivielKr~~~~~~vln~Lyk~T~Lq~s  336 (910)
                      +   ++++|+||||||++++++++|+|+++++++|++||.|++||| +++|+||||++|++++++.++++|||+|+||+|
T Consensus       230 ~---~~~~i~ItELP~g~~t~~~~e~i~~lv~~~ki~~i~~~~des~~~~~vrivI~lk~~~~~~~~~~~L~k~tkL~~s  306 (445)
T smart00434      230 D---GRNTIVITELPYQVNKAKLIEKIAELVKDKKIEGIIDVRDESHDRTGVRIVIELKRGAMAEVVLNGLYKLTKLQST  306 (445)
T ss_pred             C---CCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHEE
T ss_conf             7---9627999946876748999999999851356665010354328877526999988998989999999987201434


Q ss_pred             CCCEEEEEE-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCH-HHH
Q ss_conf             000024554-166300029999999999999999999999999998-88778999999874069999998618997-898
Q gi|254780182|r  337 FSVNMVALN-GYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKAR-DRAHVLVGLAIAVANLDEVVRIIRFSPNP-ETA  413 (910)
Q Consensus       337 f~~N~~aL~-~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~-~R~HILeGL~~Al~nIDeVI~iIR~S~d~-~eA  413 (910)
                      |++||++|+ +|+|+++++++||++|++||.++++||++|+|+|++ +|+|+++|+.++..++|+||.+||+|++. ++|
T Consensus       307 ~s~N~~~l~~~g~p~~~~~~eIL~~f~~~R~~~~~kR~~~~L~kl~~~r~~i~~~~fi~~~~~d~ii~~~r~~~~~~~~l  386 (445)
T smart00434      307 FSINMLALFDNGKPKKYNLKEILKEFLDHRLEVYTRRKEYLLGKLEAERLHILEGLFIALSIIDEIIVLIRSSKDLAKEA  386 (445)
T ss_pred             CCEEEEEEECCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCHHHHH
T ss_conf             15179999769935785259999999999999999999999999999999998869999973465776553687269999


Q ss_pred             HHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             78776312697889999974022111222344523699999999987899998887999999899999999988753049
Q gi|254780182|r  414 RRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSS  493 (910)
Q Consensus       414 k~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s  493 (910)
                      +..++++                          |.+|+.||+|||+|||+|||++|+++|++|+++|.++|++|+++|++
T Consensus       387 k~~l~~~--------------------------~~~s~~q~~yLL~M~L~~LT~~e~~kL~~E~~~l~~ei~~l~~~l~~  440 (445)
T smart00434      387 KELLMER--------------------------FELSEEQADAILDMRLRRLTKLEVEKLEKELKELEKEIEDLEKILAS  440 (445)
T ss_pred             HHHCCCC--------------------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_conf             9818866--------------------------79999999999966899872889999999999999999999846869


Q ss_pred             HHHH
Q ss_conf             8999
Q gi|254780182|r  494 RSRL  497 (910)
Q Consensus       494 ~~~l  497 (910)
                      +..+
T Consensus       441 ~~wl  444 (445)
T smart00434      441 ELWL  444 (445)
T ss_pred             HHCC
T ss_conf             6544


No 11 
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=100.00  E-value=0  Score=1148.96  Aligned_cols=443  Identities=53%  Similarity=0.847  Sum_probs=432.3

Q ss_pred             HHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCC
Q ss_conf             31375400089736789999999878999998113404255664366887047899999971220111561314788708
Q gi|254780182|r   39 GRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFG  118 (910)
Q Consensus        39 ~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfG  118 (910)
                      +|||||+|||||||||||||||++++++++++|+|||++||+|||+||||||+|+|+|||||||+||+|+||++||||||
T Consensus         2 ~RaiP~~~DGlKP~qRkiL~~~~~~~l~~~~~~~Kva~l~G~v~~~~~~HGe~sl~~aiv~mAQ~fsnn~~Ll~~~GnFG   81 (445)
T cd00187           2 GRALPDVRDGLKPVQRRILYAMFKRGLTPDKPEKKVARLVGDVAGKYHPHGDSSLYDTIVRMAQDFSNNIPLLDPQGNFG   81 (445)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCEECCCCCC
T ss_conf             87788611488789999999999707988998515510046565046898688999999998676550575331689889


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHH
Q ss_conf             87769720135789997899999986307684053306898854850343227321101676101013317898547899
Q gi|254780182|r  119 SVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEV  198 (910)
Q Consensus       119 s~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev  198 (910)
                      |++||+||||||||||||+++..||.++|+++|+|+|||||+..||+|||+.+|++|||||+|||||||||||||||.||
T Consensus        82 sr~g~~aAa~RYi~trLs~~~~~lf~~~d~~~l~y~~nyDg~~~EP~~~~p~iP~iLvNGa~GIgtG~sT~IP~hNp~ei  161 (445)
T cd00187          82 SRDGDDAAAMRYTETRLSPIARLLLPDIDDPTVDFVPNYDGQEVEPEVLPPIFPNLLVNGSSGIAVGMATNIPPHNLREV  161 (445)
T ss_pred             CCCCCCCCCHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHCCCCHHHHHCCCEEEEEEECCCCCCCCHHHH
T ss_conf             99998321034565320076999864026450335358899736742205433077634661334200056788788999


Q ss_pred             HHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHH
Q ss_conf             99998876187768888886345866887443447588999987012038999988654336784599992464435289
Q gi|254780182|r  199 VDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKA  278 (910)
Q Consensus       199 ~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~  278 (910)
                      ++|++++|++|+++.++||++++||||||||.|.+.+|+.++|+||+|++++||+|++++.+ ++++|+|||||||++++
T Consensus       162 i~~~~~~i~~~~~~~~~l~~~~~~P~f~~~g~I~~~~~~~~~~~tG~g~~~~rg~~~~~~~~-~~~~I~ITELP~g~~t~  240 (445)
T cd00187         162 IDALRALIDNPEASIDELMEIIKGPDFPTGGIIEGRAGIREAYETGRGRYIIRGKYEIEDDE-GRNTIEITELPYQVNKA  240 (445)
T ss_pred             HHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCEEECCCCCHHHEECCCCEEEEEEEEEEEECC-CCCEEEEEECCCCCCHH
T ss_conf             99998776077765788736788998999946855654012123279738997899998048-86279999558878899


Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCCCEEEEEE-CCCCCCCCHHHH
Q ss_conf             9999999998716650144587303746557999947988778999999976101100000024554-166300029999
Q gi|254780182|r  279 AMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFSVNMVALN-GYKPERFTLIGI  357 (910)
Q Consensus       279 ~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~-~g~P~~l~Lk~i  357 (910)
                      +++|+|++++++||++||+|++|+|+++|+||||++|++++++.++++|||+|+||+||++||+|++ +|+|+.+++.+|
T Consensus       241 ~~~e~i~~lv~~kk~~~I~d~~D~st~~~v~~vI~lk~~~~~~~~~~~L~k~tkL~~s~s~Nm~~~~~~g~p~~~~~~eI  320 (445)
T cd00187         241 KLKEKIAELVKDKKIEGISDVRDESDREGIRFVIELKRGAMAEVVLNGLYKVTKLQTTFGINMVAFDPNGRPKKLNLKEI  320 (445)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCHHEEECCEEEEEECCCCEEECCHHHH
T ss_conf             99999999862477874665222688772479999779866688999999871501030333899937997755069999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCC
Q ss_conf             99999999999999999999999888778999999874069999998618997898787763126978899999740221
Q gi|254780182|r  358 LKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDS  437 (910)
Q Consensus       358 L~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~  437 (910)
                      |++|++||.++++||.+|+|+++++|+|||+|+++++.+||+||++||.|+++.++..+++++                 
T Consensus       321 L~~f~~~R~~~y~kR~~~~L~kl~~rl~il~~~~~fi~~id~ii~~ir~~~~~k~~l~~~l~~-----------------  383 (445)
T cd00187         321 LQEFLDHRLEVYTRRKEYELGKAEARLHILEGLLKAILNIDEVINLIRSSDEAKKALIEELEK-----------------  383 (445)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-----------------
T ss_conf             999999999999999999999999999998649999997999999998535179999999876-----------------


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf             11222344523699999999987899998887999999899999999988753049899999999989999
Q gi|254780182|r  438 SYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSV  508 (910)
Q Consensus       438 ~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~ei  508 (910)
                               |+|++.|++|||+|||++||++|+++|++|+++|++++++|+++|+|++++++++++||.|.
T Consensus       384 ---------~~~~~~q~dyLL~M~L~~LT~~e~~kL~~e~~~l~~ei~~L~~~l~~~~~~~~~~~~EL~ef  445 (445)
T cd00187         384 ---------LGFSEIQADAILDMRLRRLTKLEREKLLKELKELEAEIEDLEKILASEERPKDLWKEELDEF  445 (445)
T ss_pred             ---------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCC
T ss_conf             ---------79999999999976699875899999999999999999999998679688999999998509


No 12 
>pfam00521 DNA_topoisoIV DNA gyrase/topoisomerase IV, subunit A.
Probab=100.00  E-value=0  Score=1083.97  Aligned_cols=423  Identities=54%  Similarity=0.849  Sum_probs=411.5

Q ss_pred             HCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCC
Q ss_conf             13754000897367899999998789999981134042556643668870478999999712201115613147887088
Q gi|254780182|r   40 RAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGS  119 (910)
Q Consensus        40 RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs  119 (910)
                      |||||++||||||||||||||++++++++++|+|||++||+|||+||||||+|+|+|||+|||+|++|+||++|||||||
T Consensus         1 RaiP~~~DGLKP~qRkil~~~~~~~l~~~~~~~Kva~l~G~v~~~YHpHGe~sl~~tiv~mAQ~f~~n~~Ll~~~GnFGs   80 (428)
T pfam00521         1 RAIPDVRDGLKPVQRRILYAMFELGLNLDKKYKKVARLVGDVMGKYHPHGDASIYDALVRMAQDFVGNIPLLDGQGNFGS   80 (428)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             99985234787899999999997278889986056433365663568885899999999986763156553216888888


Q ss_pred             C-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHH
Q ss_conf             7-769720135789997899999986307684053306898854850343227321101676101013317898547899
Q gi|254780182|r  120 V-DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEV  198 (910)
Q Consensus       120 ~-dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev  198 (910)
                      + +||+||||||||||||+++..||.++|.++|+|+|||||+..||+++|+.+|++|||||+||||||||||||||+.||
T Consensus        81 r~~g~~~AA~RYi~trLs~~~~~if~~~d~~~l~~~~~yDg~~~EP~~y~piiP~iLvNG~~GIgtG~sT~IP~hNp~ei  160 (428)
T pfam00521        81 RLDGDKAAAMRYTEARLSKIARELFKDIDKDTVDFVPNYDGSEKEPTVLPPIIPNLLVNGASGIAVGMATNIPPHNLGEV  160 (428)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHCCCCCCHHHHCCCCCCEEHEECCCCCCCHHHH
T ss_conf             88898327788999757499999976426350155057898706751106655676623787301000027788888999


Q ss_pred             HHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHH
Q ss_conf             99998876187768888886345866887443447588999987012038999988654336784599992464435289
Q gi|254780182|r  199 VDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKA  278 (910)
Q Consensus       199 ~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~  278 (910)
                      ++||+++|++|++++   +..++||||||||.+++.+++.++|+||+|+|++||+|++++    +++|+||||||+++++
T Consensus       161 i~~~~~~l~~~~~~~---~~~~~~P~f~~f~g~i~~~~~~~~y~tG~G~~~~rg~~~i~~----~~~i~ITELP~g~~t~  233 (428)
T pfam00521       161 IDALIALLDGPEITL---LLKIPGPDFPTGGGIIGSGGIREAYKTGRGKITVRAKIEIEE----RKTIVITELPYGVWTE  233 (428)
T ss_pred             HHHHHHHHCCCCCCC---CCCCCCCCCCCCCEEECCCCHHHHHHCCCCEEEEEEEEEEEC----CCEEEEEECCCCCCHH
T ss_conf             999999853997223---575789979998624566116777643883599987999940----5269999447777899


Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHH
Q ss_conf             99999999987166501445873037465579999479887789999999761011000000245541663000299999
Q gi|254780182|r  279 AMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGIL  358 (910)
Q Consensus       279 ~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL  358 (910)
                      +++|+|+++++++|+++ +|+||+||+ |+||||++|++++++.++++|||+|+||+||++||++|.|++|+.+++++||
T Consensus       234 ~~~e~l~~l~~~~ki~~-~di~D~Sd~-~vr~vI~lk~~~~~~~~~~~L~k~~kL~~s~s~nnm~l~d~~pk~~s~~eIL  311 (428)
T pfam00521       234 KLIESIEELVKNGKIKG-SDIRDESDR-GVRIVIELKRGADPEVVLNKLYKKTKLQSSFSTNNLVLFDGGPKYLNLKEIL  311 (428)
T ss_pred             HHHHHHHHHHHCCCCCC-CCCCCCCCC-CEEEEEEECCCCCHHHHHHHHHHHHHHHEECCCEEEEEECCCCCHHHHHHHH
T ss_conf             99999999984588787-731016788-5679998578765678999999863001004637999967987374299999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
Q ss_conf             99999999999999999999998887789999998740699999986189978987877631269788999997402211
Q gi|254780182|r  359 KAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSS  438 (910)
Q Consensus       359 ~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~  438 (910)
                      ++|++||.++++||++|+|+++++|+|||+||++|++++|+||++||+|.+...||..|+++                  
T Consensus       312 ~~f~~~R~~~y~kR~~~~l~kl~~~l~iL~gl~~~~~~idfIi~iI~~s~~~~~~k~~L~~~------------------  373 (428)
T pfam00521       312 KEFLEHRLEVYKRRKEYLLEKLEERLHILEGLLKALNKIDFVIEVIRGSIDLNKAKKELIEE------------------  373 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH------------------
T ss_conf             99999999999999999999999999999889999984999999997689616899999997------------------


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             1222344523699999999987899998887999999899999999988753049899999
Q gi|254780182|r  439 YTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLG  499 (910)
Q Consensus       439 ~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~  499 (910)
                                |++.|++|||+|||++||++|.++|++|+++|.+++++|+++|+|++.+|.
T Consensus       374 ----------L~~~q~dyLL~m~L~~LT~~e~~kL~~e~~~l~~ei~~l~~~l~s~~~lw~  424 (428)
T pfam00521       374 ----------LSEIQADYLLDMRLRRLTKEEIEKLEKEIEELEKEIAELEKILASEKKLWI  424 (428)
T ss_pred             ----------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf             ----------489989999976899872889999999999999999999977389999988


No 13 
>PRK12758 DNA topoisomerase IV subunit A; Provisional
Probab=100.00  E-value=0  Score=887.31  Aligned_cols=695  Identities=25%  Similarity=0.372  Sum_probs=525.5

Q ss_pred             CCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCC
Q ss_conf             87643235666009999987678777998863137540008973678999999987899999811340425566436688
Q gi|254780182|r    8 SDEEEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHP   87 (910)
Q Consensus         8 ~~~~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHP   87 (910)
                      ++++....+.+  +..--+.+||+||+|||.+||+|+++||||||||||||+|++|.   |..|.|+|+|||++| +|||
T Consensus        14 ~~~~~~~~~~~--~~gmy~~wfldYasyvil~RAvp~i~DGlKPvqRril~sm~~~~---dgr~~KvAnivG~tm-~yhP   87 (879)
T PRK12758         14 PENEPIHDTTH--VGGMYQNWFLDYASYVILERAVPHIEDGLKPVQRRILHSMKRLD---DGRYNKVANIVGHTM-QYHP   87 (879)
T ss_pred             CCCCCCHHEEE--CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH---CCCCCEEEEECCCCC-CCCC
T ss_conf             76664010245--01347888887768653352056400278538999999998610---776302320102320-2488


Q ss_pred             CCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEE
Q ss_conf             704789999997122011156131478870887-7697201357899978999999863076840533068988548503
Q gi|254780182|r   88 HGNAAIYDALARMAQDWSLRLLLIEGQGNFGSV-DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVV  166 (910)
Q Consensus        88 HGd~siy~a~v~maq~~~~r~plidg~GnfGs~-dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~v  166 (910)
                      |||+|||||||.|+|    +..|||+|||||++ +||+|||+||+|||||++|.+++  .+++|++|.++|||+.+||++
T Consensus        88 HGdasi~dalv~~~q----k~~lid~qGN~Gni~tgd~aaA~RYiE~rls~fa~ev~--fn~~~t~~~~sYDgr~kEP~~  161 (879)
T PRK12758         88 HGDASIGDALVQLGQ----KDLLIDCQGNWGNILTGDGAAAPRYIEARLSKFALEVL--FNPKTTEWQLSYDGRKKEPVT  161 (879)
T ss_pred             CCCCHHHHHHHHHHC----CCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHE--ECCCCCEEEECCCCCCCCCCC
T ss_conf             874238999998624----33368647776676878722314467564207779870--387755345456876578642


Q ss_pred             CCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCC-
Q ss_conf             4322732110167610101331789854789999998876187768888886345866887443447588999987012-
Q gi|254780182|r  167 LCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGR-  245 (910)
Q Consensus       167 lP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGr-  245 (910)
                      ||++||+||++|+.||||||||+|+|||+.|+|+|+++++++..+++-        |||||||++-     ..-|..|+ 
T Consensus       162 lP~kfPllL~~g~eGIAVGlstkilphNf~El~~a~i~~l~~~~~~l~--------PDF~tgG~~d-----~s~YndG~r  228 (879)
T PRK12758        162 LPVKFPLLLAQGVEGIAVGLSSKILPHNFNELIDASIAYLRGEEFKLY--------PDFQTGGSID-----VSNYNDGER  228 (879)
T ss_pred             CCCCCHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEC--------CCCCCCCEEC-----HHHHHCCCC
T ss_conf             552116777616762685001464887889999999999759985488--------7898875405-----645104445


Q ss_pred             -CEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHH
Q ss_conf             -0389999886543367845999924644352899999999998716650144587303746557999947988778999
Q gi|254780182|r  246 -GSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVIL  324 (910)
Q Consensus       246 -G~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vl  324 (910)
                       |++++|||++..+    ++.|||+||||++++++||++|..+.+.+||. |..|.|.+..+ +-|.|.|.+|.+|+..+
T Consensus       229 gG~v~vRaki~~~d----~~tl~I~eiP~g~tt~sLi~SI~kAn~kGKIK-Ikki~DnTa~~-VEI~i~L~~Gvs~dkti  302 (879)
T PRK12758        229 GGRVKVRAKINKLD----NKTLVITEIPYGTTTSSLIDSILKANDKGKIK-IKKVDDNTAAD-VEILVHLAPGVSSDKTI  302 (879)
T ss_pred             CCEEEEEEEEEEEC----CCEEEEEECCCCCCHHHHHHHHHHHHHCCCCC-EEEECCCCCCC-EEEEEECCCCCCHHHHH
T ss_conf             85489999999805----96699985499875799999999998759711-46632467774-06999838999878989


Q ss_pred             HHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHH
Q ss_conf             9999761011000000245541663000299999999999999999999999999988877899999987406---9999
Q gi|254780182|r  325 NQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANL---DEVV  401 (910)
Q Consensus       325 n~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nI---DeVI  401 (910)
                      ..||++|+||+|.|.|.++|.|++|..+++.++|+.-.+|-.+.+++..+.+|.+.++++|--     .|+.|   .+|.
T Consensus       303 daLYAFTdCEvSISPn~cVI~dnkP~fl~VseiLk~std~t~~LLk~ELei~l~eLeekwH~~-----SLErIFIEnRIY  377 (879)
T PRK12758        303 DALYAFTDCEVSISPNCCVIDDDKPHFLGVSEVLRISTDRTLDLLKQELEIQLEELLEQLHFA-----SLEKIFIEERIY  377 (879)
T ss_pred             HHHHHHCCCEECCCCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHH
T ss_conf             987630356220587649998994438428999999999999999999998899999999999-----899999775651


Q ss_pred             H--HHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9--98618997898787763126978899999740221112223445236999999999878999988879999998999
Q gi|254780182|r  402 R--IIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNS  479 (910)
Q Consensus       402 ~--iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~e  479 (910)
                      +  -|..+++-+++-..+-+.         +.+......        -..++.-..-.+++|.+|.++.+.+|-+++++.
T Consensus       378 rd~~IEe~~t~E~Vi~~I~~g---------L~Pf~~~L~--------ReVt~eDI~rLtEIkIkRISkFDidKa~e~I~~  440 (879)
T PRK12758        378 KDKEFEESETWEDALLHIDDR---------LEPFKKQFI--------REVTEDDILRLTEIKMKRILKFNSDKAEELIAR  440 (879)
T ss_pred             CCCHHCCCCCHHHHHHHHHHH---------HHHHHHHHC--------CCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf             440003556899999999999---------999888633--------788889999986313777554187889999999


Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCC--CCCCEEECCCCCCCC-CCCCCCCCEEEEEECCCEECCCCCCCC
Q ss_conf             99999988753049899999999989999984056--883310013434530-101456781899907970523310000
Q gi|254780182|r  480 LGIEIKECLDILSSRSRLLGIIKQELLSVKDELDT--PRRTRIVEGLLDMED-EDCIVREDMVVTVSHLGYVKRVPLSVY  556 (910)
Q Consensus       480 L~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd--~RRT~I~~~~~~i~~-EdlI~~E~vvV~lS~~GyIKr~~~~~y  556 (910)
                      |.++|++.+.-|++   +...-++-++.|+++||.  ||||+|...+. ++. .-.+.++        .=|+-|-     
T Consensus       441 le~~I~eVk~nL~n---lt~YaI~yf~~LkkKYGkg~~RKTEI~~Fd~-I~A~kVa~~N~--------KLYvNRe-----  503 (879)
T PRK12758        441 LEEDIAEVEHHLEH---IIDYTIAWFTMLKEKYGKGFPRRTELRNFDT-IEATKVVEANE--------KLYINRE-----  503 (879)
T ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHCCCCCCCCEEEECCC-EEHHHHHHHHC--------EEEEECC-----
T ss_conf             99999999988887---8999999999999986699976403410031-52777735317--------7998245-----


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEE--EECCCCCCEEEEE
Q ss_conf             02334565211000146410101133237773999954893999820004322444565541245--4536556200256
Q gi|254780182|r  557 RAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINI--LSLNQGERITTIM  634 (910)
Q Consensus       557 r~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nl--l~l~~~E~I~ail  634 (910)
                             -|..|+++|.+.   +++.|+.-|.+++|+..|++-..++-+     ..--|+.|...  ++-.+...|-.|+
T Consensus       504 -------eGFiGt~lKkdE---fv~dCSdiDDIIvF~kDG~~~VtKV~d-----K~FVGKdIihv~vfkK~D~rtiYN~I  568 (879)
T PRK12758        504 -------EGFIGTGLKKDE---FVADCSDIDDVIVFYRDGKYMVTKVAD-----KKFVGKDIIYVAVFKKNDKRTIYNVI  568 (879)
T ss_pred             -------CCEECCCCCCCC---EEEECCCCCEEEEEECCCCEEEEECCC-----CEEECCCCEEEEEEECCCCCEEEEEE
T ss_conf             -------661101324774---443035712289992388589998167-----44533675799975058873288999


Q ss_pred             EECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEE-EECCCCEEEEEEE-CCCCCEEEEEE----CCCEEEEE
Q ss_conf             630125666871799994799189842368620477722786-6158985788896-18982699993----69859997
Q gi|254780182|r  635 PFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAM-KLDSRDEILSVET-CTQENDILLTT----KLGQCVRF  708 (910)
Q Consensus       635 ~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~ai-kLkegD~Li~v~~-~~~~~~Iil~T----~~G~~lrF  708 (910)
                       +++-+           +..-++||.....+..   ....-+ +=.+|-++..... -+|+.+++-+.    ..-+-+.|
T Consensus       569 -YrDGk-----------~g~syiKRF~VtgvtR---Dk~Y~lt~g~~gSkvlYfsaNpNGEAE~V~v~Lr~~~~~kkl~~  633 (879)
T PRK12758        569 -YRDGK-----------SGPSYIKRFNVTGVTR---DKEYDLTQGTPGSRVLYFSANPNGEAEVVTVTLKPNPRIRKLVF  633 (879)
T ss_pred             -EECCC-----------CCCEEEEEEECCCEEE---CCCCCCCCCCCCCEEEEEECCCCCCEEEEEEEECCCCCCCCEEE
T ss_conf             -97388-----------8856557631241431---34024667999988999951899862689999645855341564


Q ss_pred             E--HHHCCCCCCCCCCCEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             5--87623547866553576752899869998973366654200000122233333334555444444443332222232
Q gi|254780182|r  709 P--ISAIRVFAGRNSVGVRGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNIS  786 (910)
Q Consensus       709 ~--~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  786 (910)
                      +  -+++. ..||.|+|...-|-.= -+| .                      ......+.......|.++.......+.
T Consensus       634 d~DFsdi~-IKGR~skGNivTK~~V-~kI-~----------------------lKe~G~STL~~RKIWFD~~V~RLN~d~  688 (879)
T PRK12758        634 EKDFSEIA-IKGRQSQGNILTKYPV-HKI-E----------------------LKQKGGSTLGGRKVWFDRDVLRLNYDG  688 (879)
T ss_pred             ECCHHHHH-CCCCCCCCEEEECCCE-EEE-E----------------------EECCCCCCCCCEEEEECCCCCCCCCCC
T ss_conf             13677710-0144556516750320-267-4----------------------101475555771576346423015466


Q ss_pred             CHHHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCEEEE
Q ss_conf             00111012568679999759934530178848667577414887
Q gi|254780182|r  787 EERCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGKGIRAT  830 (910)
Q Consensus       787 ~e~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgkGv~~i  830 (910)
                      ...+......+..||+++.+|--+.+.   |-+.+|-.-.+..+
T Consensus       689 RG~lLGeF~~dD~iLvi~~~G~~~~~~---~dls~hfd~d~i~l  729 (879)
T PRK12758        689 RGEYLGEFQSDDRILVILQNGEFYTTN---FELTNHYDPNMIVI  729 (879)
T ss_pred             CCCEEEECCCCCEEEEEECCCEEEECC---CCHHCCCCCCCEEE
T ss_conf             653650027886699995488189815---30312588773699


No 14 
>PTZ00108 DNA topoisomerase II; Provisional
Probab=100.00  E-value=2.8e-45  Score=423.59  Aligned_cols=468  Identities=21%  Similarity=0.333  Sum_probs=349.1

Q ss_pred             CCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHH--CCCCCCC
Q ss_conf             32356660099999876787779988631375400089736789999999878999998113404255664--3668870
Q gi|254780182|r   12 EEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVM--GKYHPHG   89 (910)
Q Consensus        12 ~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~--gkyHPHG   89 (910)
                      .+.....+++.+-+.+..+-|||+= ..|++|.+.|||||.||.|||+++.-++   +.-.|+|..+|.|-  ..|| ||
T Consensus       721 ld~~~~~i~~~dFinkELi~FS~~D-~~RSIPs~~DGlKp~QRKvl~~~fkrn~---~~eiKVaQlaGyVse~saYH-HG  795 (1506)
T PTZ00108        721 VDHKEKDLSYYDFVNKELIYYSRYD-TERSIPNIMDGWKPGQRKVLYGCFKRNL---KNECKVAQLVGYIAEHSAYH-HG  795 (1506)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCHHH-HHHHCCHHHCCCCHHHHHHHHHHHHHCC---CCCEEHHHHHHHHHHHCCCC-CC
T ss_conf             3566785438774437888642887-6512411330577124424498786347---76223215088987630467-63


Q ss_pred             HHHHHHHHHHHCCCH--HCCCCCCCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCE
Q ss_conf             478999999712201--1156131478870887--769720135789997899999986307684053306898854850
Q gi|254780182|r   90 NAAIYDALARMAQDW--SLRLLLIEGQGNFGSV--DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPV  165 (910)
Q Consensus        90 d~siy~a~v~maq~~--~~r~plidg~GnfGs~--dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~  165 (910)
                      ++|...|+|.|||+|  |++.+|+.+-|+|||.  .|.-+||+||+.++|++++..++..-|.....|. +=||...||+
T Consensus       796 E~SL~~tIv~mAQ~fvGsNNinlL~P~GqFGtR~~GGkDaas~RYIfT~l~~~~r~iF~~~Dd~lL~y~-~ddg~~iEP~  874 (1506)
T PTZ00108        796 ESSLQQTIINMAQTFVGSNNINFLEPCGQFGSRKEGGKDASAARYIFTKLASSTRSIFNEYDDPILKYL-NEEGQKIEPQ  874 (1506)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHCCCCCHHHHHCC-CCCCCCCCCC
T ss_conf             899999999998753565663104557875254558875556025766315888853893302255020-3689631543


Q ss_pred             -ECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             -3432273211016761010133178985478999999887618776888888634586688744344758899998701
Q gi|254780182|r  166 -VLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATG  244 (910)
Q Consensus       166 -vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tG  244 (910)
                       ++|. +|.+||||+.||++||+|+|||||+.||++.+..+|+..+..  .+.-+-+|  | +|-+          .++|
T Consensus       875 ~Y~Pi-iPmvLvNG~~GIGTGwSt~ip~ynp~dii~ni~r~l~ge~~~--~m~Pwy~g--f-~G~i----------~~~~  938 (1506)
T PTZ00108        875 YYIPV-IPTILVNGCEGIGTGYSSFIPNYNYKDIIDNIKRYINKEPLI--PMIPWYKD--F-KGRI----------ESNG  938 (1506)
T ss_pred             EECCC-CCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCC--CCCCCCCC--C-CCEE----------EECC
T ss_conf             02055-667873377620266347789999999999999985699886--27755379--6-2169----------9868


Q ss_pred             CCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHH
Q ss_conf             20389999886543367845999924644352899999999998716650144587303746557999947988778999
Q gi|254780182|r  245 RGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVIL  324 (910)
Q Consensus       245 rG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vl  324 (910)
                      .+++++.|.++..    +.+.|.|||||-.+-....-|.+..++.+++-+-|.|.+++++-..++++|.+....-.+..-
T Consensus       939 ~~~y~~~G~~~~~----~~~t~~ItELPi~~WT~~yKe~le~~~~~~~~~~i~d~~e~~t~~~V~F~i~~~~~~~~~~~~ 1014 (1506)
T PTZ00108        939 KTGYETIGIIHKI----DDDTLEINELPIKKWTQDYKEFLEELLTDEKHQLILDYIDNSSHEDICFTIKMDPAKLKKAEE 1014 (1506)
T ss_pred             CCEEEEEEEEEEE----CCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHCCCCCEEEEEEEECHHHHHHHHH
T ss_conf             9718998799995----798799985898762699999999875046777400004317997589999958899899876


Q ss_pred             HHHHHHCCHHCCCCC-EEEEEE-CCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH
Q ss_conf             999976101100000-024554-166-300029999999999999999999999999998887789999998740-6999
Q gi|254780182|r  325 NQLYRYTSLQSLFSV-NMVALN-GYK-PERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVAN-LDEV  400 (910)
Q Consensus       325 n~Lyk~T~Lq~sf~~-N~~aL~-~g~-P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~n-IDeV  400 (910)
                      .-|.+.-.|+++++. ||++.. .|+ -+--+..+||++|...|.+...+|-.|.|.+.+..+.+|+--..-+.. ||. 
T Consensus      1015 ~gl~k~fKL~~~i~t~Nm~~Fd~~g~i~kY~~~~~Il~eF~~~Rl~~Y~kRK~~l~~~l~~~~~~l~nqaRFI~~vi~~- 1093 (1506)
T PTZ00108       1015 EGLEKVFKLKSTLTTTNMTLFDPNLKLQRYSTELDILKDFCFHRLKAYENRKSYLISKLEKEKKIISNKSKFILAIVNN- 1093 (1506)
T ss_pred             HCHHHHHCCCCEEEECCEEEECCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-
T ss_conf             0666651123134205268988999966459999999999999999999999999999999999864255656640067-


Q ss_pred             HHHHHHCCCHHHHHHHHHHHCCCHHH-HHHHH-HHC-------CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99986189978987877631269788-99999-740-------2211122234452369999999998789999888799
Q gi|254780182|r  401 VRIIRFSPNPETARRELMQRSWNASD-IKDLI-DLI-------DDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       401 I~iIR~S~d~~eAk~~L~~~~~~~~~-~~~~~-~~~-------~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                       +++=+-+.+++--..|.++.|..-. ..... ...       .....+......-+++..--+++|.|+|..||.--.+
T Consensus      1094 -~l~v~nkkk~~li~eL~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ydYLL~M~iwsLT~Er~~ 1172 (1506)
T PTZ00108       1094 -ELIVNKKKKKVLVEELYRKGYDPYKDINKIKKEEIFEQELLDAADNPEDNEEIIAGISVKDYDYLLSMPIFSLTLEKVE 1172 (1506)
T ss_pred             -EEEEECCCHHHHHHHHHHCCCCCCCCHHHHHHHCCCHHHHHCCCCCCCCCHHHCCCCCCCCCHHHHCCCHHHCCHHHHH
T ss_conf             -5899357689999999974999774112433301000221012235544201014677678436638812320099999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             99998999999999887530498999999999899999840
Q gi|254780182|r  472 DIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDEL  512 (910)
Q Consensus       472 kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~ky  512 (910)
                      +|..+.++..++.+.|...  +++.+|.-   +|.++-+.|
T Consensus      1173 ~L~~~~~~k~~El~~L~~~--s~~dlW~~---DLd~fee~~ 1208 (1506)
T PTZ00108       1173 DLLAQHKEKEKELEILKNI--TVETMWLK---DIEKVEEAI 1208 (1506)
T ss_pred             HHHHHHHHHHHHHHHHHCC--CHHHHHHH---HHHHHHHHH
T ss_conf             9999999999999999768--98999999---999999999


No 15 
>KOG0355 consensus
Probab=100.00  E-value=2.6e-42  Score=397.72  Aligned_cols=752  Identities=11%  Similarity=-0.035  Sum_probs=579.7

Q ss_pred             CCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCH
Q ss_conf             43235666009999987678777998863137540008973678999999987899999811340425566436688704
Q gi|254780182|r   11 EEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGN   90 (910)
Q Consensus        11 ~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd   90 (910)
                      ..+-+++++.|..|-...++-|+-++|-.|+.|+.+++++|+++++|++|+..+-...|++.+|++.++.+.+.+|||++
T Consensus        71 d~~m~~i~v~i~~e~~~isv~nnGkGIPv~~H~~ek~yvpelifg~Lltssny~d~ekK~tggrngygakLcniFs~~f~  150 (842)
T KOG0355          71 DPKMNTIKVTIDKEKNEISVYNNGKGIPVTIHKVEKVYVPELIFGNLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFT  150 (842)
T ss_pred             CCCCCEEEEEECCCCCEEEEEECCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCCE
T ss_conf             87765268887167767999957972131223422245347887664411567887543236777502034321145403


Q ss_pred             HHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHHCCCCCCCCEECCCCCCCCCEECCC
Q ss_conf             78999999712201115613147887088776972013578999789999-99863076840533068988548503432
Q gi|254780182|r   91 AAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAH-FLLDDLGKDTVDFRPNYDGSFQEPVVLCA  169 (910)
Q Consensus        91 ~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~-~~l~~i~~~tv~~~~n~D~~~~EP~vlP~  169 (910)
                      ..+||..++|||-++.+-++.-+|++|++.+.|++    ||+||++|-.+ ..+.++|.|||+++.+++-...+|. +|+
T Consensus       151 ~Et~d~~~~~~~kQ~w~~nm~~~~~~~i~~~~~~~----yTkitF~PDl~~F~m~eLD~Div~l~~rr~~d~a~~~-~~v  225 (842)
T KOG0355         151 VETADREYKMAFKQTWINNMTRDEEPKIVPSTDED----YTKITFSPDLEKFKMKELDDDIVALMARRAYDLAGSV-KSV  225 (842)
T ss_pred             EEEEEHHHHHHHHHHHHCCCCCCCCCEEECCCCCC----CCEEEECCCHHHCCCHHHCCHHHHHHHHHHHHHCCCC-CCE
T ss_conf             65300677778777652687656786552258999----5369968476752722322318876776666523442-121


Q ss_pred             CCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             27321101676101013317898547899999988761877688888863458668874434475889999870120389
Q gi|254780182|r  170 RYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIV  249 (910)
Q Consensus       170 ~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~  249 (910)
                      ++|..+-|++++++++||+++|| |+  -.+..+.+|.++...--|+.-...-++|++  +..........+-|+.+-++
T Consensus       226 kv~ln~~~~~~~~f~~yv~~~~~-~~--~~~~~~~~ihe~~~~RwEv~~a~s~~~fqq--isfvNsI~T~kGGThVd~V~  300 (842)
T KOG0355         226 KVELNGKNIPVKGFYDYVKMYLE-VL--WLNDDLKPLHEVLNFRWEVALALSDVGFQQ--VSFVNSIATTKGGTHVDYVV  300 (842)
T ss_pred             EEEECCCCCCCHHHHHHHHHCCC-CC--CCCCCCHHHHCCCCHHHHHHHHHCCCCCCE--EEEECCCEECCCCCCCCHHH
T ss_conf             56516887752017788762353-22--246752222004324888865504466533--54200101047986544166


Q ss_pred             EEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             99988654336784599992464435289999999999871665014458730374655799994798877899999997
Q gi|254780182|r  250 IRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYR  329 (910)
Q Consensus       250 iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk  329 (910)
                      -+.+..+++.-..++.-.++++||+.+|+.|.-.|..++.+...++.++.++.++..+.+.+.+|+....+...++. +-
T Consensus       301 D~iv~~l~~vvkKk~~~~~~svk~f~vkn~L~vfVN~lIENPtFesQTke~lt~~~~~fgs~~elsek~~k~~~~~~-i~  379 (842)
T KOG0355         301 DQIVAKLIDVVKKKKVKKDISVKPFQVKNHLWVFVNCLIENPTFESQTKERLTLRPKRFGSDCELSEKFTKAIELKG-VV  379 (842)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCHHHHHCCEEEEEEEEECCCCCCCCCHHHCCCCCCCCCCEEEEHHHHHHHHHHCC-HH
T ss_conf             55777888874211346654446453303569999887427663443310126663454326763167799998676-49


Q ss_pred             HCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             61011000000245541663000299999999999999999999999999988877899999987406999999861899
Q gi|254780182|r  330 YTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPN  409 (910)
Q Consensus       330 ~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d  409 (910)
                      .+-+|.++++++..|.+++|+.++..+-+..+.+.+....+ +..+-..-+.++-|..++-+-.+...++.+--|=-   
T Consensus       380 esils~s~~~~~~dL~kk~~~~~s~~e~I~KleDa~~ag~k-~s~kctlIltEgdsaksLavsGl~vvgRd~~gVfp---  455 (842)
T KOG0355         380 ESILSKSLNKYKDDLAKKRGKLTSRSKGIPKLEDANDAGTK-TSEKCTLILTEGDSAKSLAVSGLSVVGRDYYGVFP---  455 (842)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCC-CCCCEEEEEECCCCCHHHEECCCCCCCEEEEEECC---
T ss_conf             99999888889876544434443320130676523324434-55431688861552033201355546604675501---


Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78987877631269788999997402211122234452369999999998789999888799999989999999998875
Q gi|254780182|r  410 PETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLD  489 (910)
Q Consensus       410 ~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~  489 (910)
                         ++..|.+                    .........+...|++||+..=..++++.+..   .|--.+-+.|-....
T Consensus       456 ---lrgklLN--------------------v~e~s~kqilkn~EI~aIikIlgl~~~~~y~~---~eslryg~~mimtDQ  509 (842)
T KOG0355         456 ---LRGKLLN--------------------VREASHKQILKNAEINAIIKILGLQYKKKYFD---VESLRYGKLMIMTDQ  509 (842)
T ss_pred             ---CCCCHHH--------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCCHHHEEEEECC
T ss_conf             ---1231344--------------------57777988877999999999998877533133---122242224665123


Q ss_pred             HHCCHHHHHHHHHHH-HHHHHHHCCCCCCCEEECCCC-CCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCC
Q ss_conf             304989999999998-999998405688331001343-453010145678189990797052331000002334565211
Q gi|254780182|r  490 ILSSRSRLLGIIKQE-LLSVKDELDTPRRTRIVEGLL-DMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRS  567 (910)
Q Consensus       490 IL~s~~~l~~iI~~E-L~eik~kygd~RRT~I~~~~~-~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~  567 (910)
                       .-|-+.+..+|++- ..+....|..|   -|++... .+..++-++++.   ..|-.+|.|+....++ .|+++-|+.+
T Consensus       510 -d~dgshikgllInf~~~~~psl~~~~---fleefitpi~k~~~~~~~~~---fys~pey~kw~~~~~~-~~~~~ikyyk  581 (842)
T KOG0355         510 -DHDGSHIKGLLINFIHHFWPSLLQIP---FLEEFITPIVKATKGKQEVS---FYSLPEYEKWKKNTDN-WKSWKIKYYK  581 (842)
T ss_pred             -CCCCCHHHHHHHHHHHHHHHHHHCCC---CHHHCCCCCEEECCCCCCEE---EECCHHHHHHHHCCCC-CCCCCEEEEE
T ss_conf             -45643477788988987658863587---42104776457404774314---5445657888754844-2442237751


Q ss_pred             CCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCE
Q ss_conf             00014641010113323777399995489399982000432244456554124545365562002566301256668717
Q gi|254780182|r  568 GVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLY  647 (910)
Q Consensus       568 ~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~  647 (910)
                      |..+...|.....|.|..|+.++||.+.|..+....+.+|..++.+++++|.++.+...+ +.+..+++++|-    +.+
T Consensus       582 glgts~~~e~keyf~~~~~h~~~F~~~~~~d~~~i~~af~k~k~~~rk~wL~~~~~~~~~-~~~~~v~~sdf~----~el  656 (842)
T KOG0355         582 GLGTSTSKEAKEYFSDLDRHRILFKYDGGIDDEAIDMAFSKKKIDARKEWLRKYMPEYLY-KTTKFVTISDFV----KEL  656 (842)
T ss_pred             CCCCCCHHHHHHHHHCHHHHEEEEECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHCC-CCCCEEEHHHHH----HHH
T ss_conf             477454789999861600123787525750477886422310066677689986566413-665255789999----999


Q ss_pred             EEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEE
Q ss_conf             99994799189842368620477722786615898578889618982699993698599975876235478665535767
Q gi|254780182|r  648 VVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGI  727 (910)
Q Consensus       648 Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgI  727 (910)
                      ++|.+.+ -|+.+...-+..+|+.+..++++.+++|+-.|+++.-.+.+.....+++.+.-.+-.++.    ...|    
T Consensus       657 ilf~~~~-sIp~~~dglkpgqRkv~~~~~k~n~~~E~Kv~ql~g~v~~~s~yhhge~sl~~ti~~l~q----~~~g----  727 (842)
T KOG0355         657 ILFSNAD-SIPSLVDGLKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQSLMSTIVNLAQ----DFVG----  727 (842)
T ss_pred             HHHHHCC-CCHHHHHCCCCCCHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHCCCHHHHHHHHHHHH----HHCC----
T ss_conf             9987215-207677235866223346767644766255433024788888774342769999998887----5058----


Q ss_pred             ECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCC
Q ss_conf             52899869998973366654200000122233333334555444444443332222232001110125686799997599
Q gi|254780182|r  728 SLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEKG  807 (910)
Q Consensus       728 kL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G  807 (910)
                          .|    +     +.+.      |.     .                    +  .....-.......++.|+.-++|
T Consensus       728 ----kd----a-----a~~r------yi-----~--------------------t--~l~~~tr~~f~~~dd~ll~~~~~  761 (842)
T KOG0355         728 ----KD----A-----ASAR------YI-----F--------------------T--KLSPLTRLLFPPADDLLLKYLNE  761 (842)
T ss_pred             ----CC----C-----HHHH------HH-----H--------------------H--HCCHHHHHCCCCCCHHHHHHHCC
T ss_conf             ----84----0-----2367------89-----8--------------------8--52736540278883267665225


Q ss_pred             CEEEEEHHHCCCCCC-----CCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEE
Q ss_conf             345301788486675-----774148876067777686899997289964999945998999990105544515687388
Q gi|254780182|r  808 FGKRTSSYDFRISNR-----SGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVI  882 (910)
Q Consensus       808 ~GKRt~~~eyr~q~R-----GgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i  882 (910)
                      +|+|++.+ |+.---     |+.|+=         +|- ..-.++-+..||+.....+..-+ ++.+++++.|...|..-
T Consensus       762 ~~~~vep~-y~pi~p~vlvngaegiG---------tGw-s~~i~n~n~~~iv~~~r~~~~~~-~~~~~~p~yr~frg~i~  829 (842)
T KOG0355         762 DGQRVEPE-YCPIIPMVLVNGAEGIG---------TGW-STFIPNYNPREIVKNIRRLINGE-PPKAMAPWYRNFRGTIE  829 (842)
T ss_pred             CCCCCCCC-CCCCEEEEEEECCCCCC---------CCC-CCCCCCCCHHHHHHHHHHHHCCC-CCCCCCCHHHHCCEEEE
T ss_conf             78671752-24414688850565455---------676-56688889899999998863699-85217803520442799


Q ss_pred             E
Q ss_conf             9
Q gi|254780182|r  883 F  883 (910)
Q Consensus       883 ~  883 (910)
                      .
T Consensus       830 ~  830 (842)
T KOG0355         830 V  830 (842)
T ss_pred             E
T ss_conf             9


No 16 
>PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated
Probab=99.94  E-value=4.9e-24  Score=234.12  Aligned_cols=240  Identities=21%  Similarity=0.286  Sum_probs=162.0

Q ss_pred             CCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCE---EEEEECCCCEEEEECCCCCCCCCC
Q ss_conf             78189990797052331000002334565211000146410101133237773---999954893999820004322444
Q gi|254780182|r  536 EDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTS---VLFFSSLGFVYKEKVWRLPIGSPQ  612 (910)
Q Consensus       536 E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~---LLfFTs~Gkvy~l~v~~IP~~sr~  612 (910)
                      ...++..|+.|+|||++++.|+. +|+|  ..+++++++|.+..+..|...+.   +++.|..|.++...--++...+|+
T Consensus       622 ~~~lvfaTk~G~VKKt~L~~f~~-~~sg--iiAIkL~egDeLI~V~l~~~~~~~~~i~l~T~~G~~irf~e~~vR~mGR~  698 (959)
T PRK13979        622 QKDFIFITDSGGIKKTSLDKFNT-NYSK--LMALKLKKGEELIKVKLVDRTREEKFLKIKTKKGLSFTVEEPELEPVDRN  698 (959)
T ss_pred             CCEEEEEECCCEEECCCHHHCCC-CCCC--CEEEECCCCCEEEEEEEECCCCCCEEEEEECCCCEEEECCCHHCCCCCCC
T ss_conf             75499992898688373898285-5678--36666699987987897358887507999658965997142022457876


Q ss_pred             CCCCC---------------------------------------------------------------------------
Q ss_conf             56554---------------------------------------------------------------------------
Q gi|254780182|r  613 ARGKA---------------------------------------------------------------------------  617 (910)
Q Consensus       613 skG~p---------------------------------------------------------------------------  617 (910)
                      +.|.-                                                                           
T Consensus       699 a~GVrgi~L~~~D~Vvsm~i~~~~e~~~~~~~i~~~g~i~~~~~~~~~~~~~~~~~~~~~ili~~~~G~~~~~~~~~~~~  778 (959)
T PRK13979        699 ILGYQLFNLSPNDSIKKVDFCDNYEYKEFYININKKGIIKISDLKKNKSHISLKTNSSKNLLLFSDKGKVYKIPAFMLQN  778 (959)
T ss_pred             CCCEEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEECCCCCEEECCHHHCCC
T ss_conf             66752143399998986102244420000023342002332210011111111356631135432577233032432023


Q ss_pred             -------CEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEE
Q ss_conf             -------124545-365562002566301256668717999947991898423686204777227866158985788896
Q gi|254780182|r  618 -------LINILS-LNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVET  689 (910)
Q Consensus       618 -------i~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~  689 (910)
                             +..+.. +..+|.|++++++..+   .++.+++.+|++|++|||++.+|....+.|+....-.+.|.++++..
T Consensus       779 ~~~~g~~i~~~~~~~~~~e~vi~~~~~~~~---~e~~~il~vTe~G~GKRT~~~eyr~~g~~~~~~k~~~~~~~~v~~~~  855 (959)
T PRK13979        779 IEESGINISALTGDFEKKESIINAISIFEF---EEDLSIYFFSKKGLVKKTLLSEFKGEGNSTQVYKFKHKEDELVSVDI  855 (959)
T ss_pred             CCCCCCCCHHHHHHHCCCCCEEEEEECCCC---CCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEEEEECCCCEEEEEE
T ss_conf             355564502222121022302466520357---77615999935897466656773346786489998844897899997


Q ss_pred             -CCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             -1898269999369859997587623547866553576752899869998973366654200000122233333334555
Q gi|254780182|r  690 -CTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGD  768 (910)
Q Consensus       690 -~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~  768 (910)
                       ..++++|+++|++|+++||+.+++|.+ ||+|+||++|+|+++|+||++.++.+.+.                      
T Consensus       856 ~~~~~d~imliT~~G~~IR~~v~~I~~~-GR~tqGV~li~L~~~dkVV~~~~i~~~~~----------------------  912 (959)
T PRK13979        856 NEHEQKNILIITKKGMAIRFKSEAVNPM-GKIASGVTGISLKDEDKVIFGSIIDENDT----------------------  912 (959)
T ss_pred             ECCCCCEEEEEECCCEEEEEEHHHCCCC-CCCCCCEEEEECCCCCEEEEEEEECCCCC----------------------
T ss_conf             0489963899907987999872434702-60368806897389987999999747777----------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCEEEEECC
Q ss_conf             44444444333222223200111012568679999759934530178848667577414887606
Q gi|254780182|r  769 TEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGKGIRATDVS  833 (910)
Q Consensus       769 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~  833 (910)
                                                   ..|.+.|.+|.+|-+.+.+...|||+|+|...|-+.
T Consensus       913 -----------------------------~~~~~~~k~~~~~~~~~~~~~~q~~~g~g~~~~~~~  948 (959)
T PRK13979        913 -----------------------------RKIKLKSKAKDKGEIEIEDIKLQNRAGRGNSLMPLL  948 (959)
T ss_pred             -----------------------------CEEEEEECCCCCCEEEHHHHHHCCCCCCCCEEEEEE
T ss_conf             -----------------------------459999738866278711311000267872478862


No 17 
>PRK05560 DNA gyrase subunit A; Validated
Probab=99.92  E-value=7.2e-23  Score=223.69  Aligned_cols=199  Identities=24%  Similarity=0.390  Sum_probs=145.4

Q ss_pred             CCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCC
Q ss_conf             67818999079705233100000233456521100014641010113323777399995489399982000432244456
Q gi|254780182|r  535 REDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQAR  614 (910)
Q Consensus       535 ~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~sk  614 (910)
                      ++..++.+|++|+|||++++.|...++  .|+.+++++++|.+..+..|+..+.++++|+.|++...+..++|..+|+++
T Consensus       608 ~~~~Lv~~Tk~G~IKRt~L~df~~~r~--~G~~AikLke~DeLv~v~l~~~~~dIil~T~~G~alRF~~~eVR~~GR~a~  685 (822)
T PRK05560        608 DDLYLFFATKNGTVKKTALSEFSNIRS--NGLIAINLDEGDELIGVRLTDGDDDVLLFSANGKAIRFPEEDVRPMGRTAR  685 (822)
T ss_pred             CCCEEEEEECCCCEEEECHHHCCCCCC--CCEEEEECCCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCC
T ss_conf             885699995797279713687225552--551999858997799999848998799997897399950665777788776


Q ss_pred             CCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCC--CEEEEEEC-CCCEEEEEEECC
Q ss_conf             554124545365562002566301256668717999947991898423686204777--22786615-898578889618
Q gi|254780182|r  615 GKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRS--GKIAMKLD-SRDEILSVETCT  691 (910)
Q Consensus       615 G~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~--G~~aikLk-egD~Li~v~~~~  691 (910)
                      |.--   +.|.++++|+++..+++      +.+|+++|++|++|||++++|...++.  |.++|++. .++.|+++..+.
T Consensus       686 GVkg---IkL~~gD~VV~~~vv~~------~~~iL~vTe~G~GKRt~~~eyr~~~RGgkGv~~ik~~~k~G~lv~~~~V~  756 (822)
T PRK05560        686 GVRG---IKLREGDEVVSMSVLRD------EQFVLTVTENGYGKRTPAEEYRLQGRGGKGVIAIKITERNGKLVGAVPVD  756 (822)
T ss_pred             CCCC---EECCCCCEEEEEEEECC------CCEEEEEECCCEEEECCHHHCCCCCCCCCCEEEEEECCCCCCEEEEEECC
T ss_conf             8431---55199998999998579------98799991898053052888375577877758899648888489999917


Q ss_pred             CCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCCEEEEEEEECCCC
Q ss_conf             982699993698599975876235478665535767528998699989733666
Q gi|254780182|r  692 QENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGDQVISMAIVLHAD  745 (910)
Q Consensus       692 ~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~  745 (910)
                      ++++|+++|+.|+++|++.+++|. +||+|+||+.|+|+++|+|++.+.+...+
T Consensus       757 ~~deI~liT~~G~~iRi~v~~I~~-~gR~t~GVrl~~L~~~d~v~~va~v~~~~  809 (822)
T PRK05560        757 DDDEIMLITDAGKLIRTRVSEIRI-TGRNTQGVTLIRLDEGEKVVSVARVAEEE  809 (822)
T ss_pred             CCCEEEEEECCCEEEEEEHHHCCC-CCCCCCCEEEEECCCCCEEEEEEEECCCC
T ss_conf             998699992798799987100475-67578870899859999899999807876


No 18 
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=99.91  E-value=3.9e-22  Score=217.13  Aligned_cols=192  Identities=19%  Similarity=0.337  Sum_probs=98.6

Q ss_pred             EEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCE-EEEEECCCCEEEEECC--CCCCCCCCCC
Q ss_conf             189990797052331000002334565211000146410101133237773-9999548939998200--0432244456
Q gi|254780182|r  538 MVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTS-VLFFSSLGFVYKEKVW--RLPIGSPQAR  614 (910)
Q Consensus       538 vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~-LLfFTs~Gkvy~l~v~--~IP~~sr~sk  614 (910)
                      .++..|++|+|||+.+++|..-+  ..|+.++++.|+|.+..+..|...|. +++||.+|++...+.-  ++-..+|++.
T Consensus       636 yl~~aTk~G~vKk~~L~~F~~~r--s~GiiAi~L~e~D~L~~v~~~~~~~~~v~l~s~~G~~~RF~~~~~~vR~mgR~~~  713 (864)
T TIGR01063       636 YLFLATKNGVVKKTSLTEFSNIR--SNGIIAIKLDEGDELISVRLVDGDDEKVMLGSKNGKAVRFPEEDEEVREMGRATR  713 (864)
T ss_pred             EEEEECCCCEEEEEECHHHHHHH--HCCEEEEEEECCCEEEEEEEEECCCCEEEEEECCCCEEECCCCCCCHHCCCCCCC
T ss_conf             79997267438874001443545--2786999970896899999960788658865148847983688531100245567


Q ss_pred             CCCCEEEEECCCC----------------------------CCEEEEEEECCCCCCCCCC-EEEEEECCCCEEEECHHHH
Q ss_conf             5541245453655----------------------------6200256630125666871-7999947991898423686
Q gi|254780182|r  615 GKALINILSLNQG----------------------------ERITTIMPFPEDESSWNNL-YVVFATKHGNVRRNKLSDF  665 (910)
Q Consensus       615 G~pi~nll~l~~~----------------------------E~I~ail~~~~~~~~~~~~-~Lvl~Tk~G~VKkt~l~ef  665 (910)
                      |.-=   ++|..+                            +.++++..++      ++. +|+.+|.||+.|||++++|
T Consensus       714 GV~G---i~L~~~~~v~~~~~~~~i~~~~~D~~~~~L~~NlD~vv~~~~~~------e~~~~lL~vt~nGyGKRt~~~~y  784 (864)
T TIGR01063       714 GVRG---IKLKNEDSVISMTVLKGINSIKEDRNLEELGVNLDFVVSLEVVS------EESQKLLIVTENGYGKRTSIEEY  784 (864)
T ss_pred             CEEE---EEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEC------CCCCEEEEEEECCCCEECCHHHC
T ss_conf             6013---54067774000134432120022224654374243447778624------99837899830684200426257


Q ss_pred             HHCCCCC--EEEEEEC-CCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCCEEEEEEEE
Q ss_conf             2047772--2786615-89857888961898269999369859997587623547866553576752899869998973
Q gi|254780182|r  666 IQINRSG--KIAMKLD-SRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGDQVISMAIV  741 (910)
Q Consensus       666 ~~~r~~G--~~aikLk-egD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi  741 (910)
                      ....++|  .+.++.. .+..||+|..++++|+|+++|+.|+++|.+.++||. +||+|+|||.|+|+++|.|+++..+
T Consensus       785 r~~~RGg~Gv~~~~~~~r~G~vVga~~V~~~d~lm~iT~~G~~iR~~~~~vs~-~GR~t~GVrL~~l~e~d~vv~v~~~  862 (864)
T TIGR01063       785 RLQSRGGKGVKSIKITDRNGQVVGAIAVDDDDELMLITSSGKLIRTSVQDVSI-QGRNTQGVRLIRLDEDDKVVSVSLV  862 (864)
T ss_pred             CCCCCCCCEEEEEEEECCCCCEEEEEEECCCCHHHHEECCCCEEEEEEEHHCC-CCCCCCCEEEEEECCCCCEEEEEEC
T ss_conf             63265662378899864689687898745874000101088379976103211-5653565589851787635642202


No 19 
>KOG0355 consensus
Probab=99.86  E-value=1.5e-21  Score=211.99  Aligned_cols=185  Identities=31%  Similarity=0.477  Sum_probs=154.5

Q ss_pred             EEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHH--HCCCCCCCHHHHH
Q ss_conf             66009999987678777998863137540008973678999999987899999811340425566--4366887047899
Q gi|254780182|r   17 TSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEV--MGKYHPHGNAAIY   94 (910)
Q Consensus        17 ~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v--~gkyHPHGd~siy   94 (910)
                      ..+++.+-. +.|+-++|.=    .+|.+.|||||-||.+||...+.+.   +.-.|.|+.+|-|  +.-|| ||.+|.-
T Consensus       645 ~~v~~sdf~-~elilf~~~~----sIp~~~dglkpgqRkv~~~~~k~n~---~~E~Kv~ql~g~v~~~s~yh-hge~sl~  715 (842)
T KOG0355         645 KFVTISDFV-KELILFSNAD----SIPSLVDGLKPGQRKVLFTCFKRND---KREVKVAQLAGSVAEMSAYH-HGEQSLM  715 (842)
T ss_pred             CEEEHHHHH-HHHHHHHHCC----CCHHHHHCCCCCCHHHHHHHHHHCC---CCCEEEEEECCHHHHHHHHH-CCCHHHH
T ss_conf             255789999-9999987215----2076772358662233467676447---66255433024788888774-3427699


Q ss_pred             HHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCC
Q ss_conf             99997122011156131478870887769720135789997899999986307684053306898854850343227321
Q gi|254780182|r   95 DALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNV  174 (910)
Q Consensus        95 ~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~l  174 (910)
                      .|.|+|||+|..                .+||+.||.+..|++.+.-++.--|.....|. |=||...||+++|. +|++
T Consensus       716 ~ti~~l~q~~~g----------------kdaa~~ryi~t~l~~~tr~~f~~~dd~ll~~~-~~~~~~vep~y~pi-~p~v  777 (842)
T KOG0355         716 STIVNLAQDFVG----------------KDAASARYIFTKLSPLTRLLFPPADDLLLKYL-NEDGQRVEPEYCPI-IPMV  777 (842)
T ss_pred             HHHHHHHHHHCC----------------CCCHHHHHHHHHCCHHHHHCCCCCCHHHHHHH-CCCCCCCCCCCCCC-EEEE
T ss_conf             999988875058----------------84023678988527365402788832676652-25786717522441-4688


Q ss_pred             HHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEE
Q ss_conf             10167610101331789854789999998876187768888886345866887443447588999987012038999
Q gi|254780182|r  175 LVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIR  251 (910)
Q Consensus       175 L~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR  251 (910)
                      |+||+.||+.||+|.||++|..||+.-+..++++.+.  .                     .|...|+.-||++.+-
T Consensus       778 lvngaegiGtGws~~i~n~n~~~iv~~~r~~~~~~~~--~---------------------~~~p~yr~frg~i~~~  831 (842)
T KOG0355         778 LVNGAEGIGTGWSTFIPNYNPREIVKNIRRLINGEPP--K---------------------AMAPWYRNFRGTIEVI  831 (842)
T ss_pred             EEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC--C---------------------CCCCHHHHCCEEEEEE
T ss_conf             8505654556765668888989999999886369985--2---------------------1780352044279995


No 20 
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=99.85  E-value=9.9e-19  Score=186.69  Aligned_cols=188  Identities=23%  Similarity=0.373  Sum_probs=156.6

Q ss_pred             CEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEE
Q ss_conf             17999947991898423686204777227866158985788896189826999936985999758762354786655357
Q gi|254780182|r  646 LYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVR  725 (910)
Q Consensus       646 ~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVk  725 (910)
                      ...|.+|++|+|||++...+      +...++++++|.+...+.++..+.++++|+.|++...+..+++  .|| ++|.-
T Consensus       509 ~v~V~lS~~GyIKr~k~~~~------~~~~~~~Ke~D~v~~~~~~~T~d~LLfFTn~Grvy~lkv~~IP--~~r-~~G~p  579 (745)
T PRK05561        509 PVTVVLSKKGWVRRAKGHDI------DPAGLGYKEGDSLLFAFEARTTDKLLFFTSTGRVYSLPVHELP--SAR-GQGEP  579 (745)
T ss_pred             CCEEEECCCEEEEEECCCCC------CCCCCCCCCCCCEEEEEEEECCCEEEEEECCCEEEEEEHHHCC--CCC-CCCCC
T ss_conf             61899817804998448886------7544567778532589998069769999579759998922087--866-78808


Q ss_pred             ---EEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEE
Q ss_conf             ---67528998699989733666542000001222333333345554444444433322222320011101256867999
Q gi|254780182|r  726 ---GISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILT  802 (910)
Q Consensus       726 ---gIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~  802 (910)
                         .+.|.++++|+++..+.                                                     +++++++
T Consensus       580 i~nll~L~~~EkIv~vl~~~-----------------------------------------------------~~~~lll  606 (745)
T PRK05561        580 LTGLIDLEPGEEIVHVLVGD-----------------------------------------------------PDQKLLL  606 (745)
T ss_pred             HHHCCCCCCCCEEEEEEEEC-----------------------------------------------------CCCEEEE
T ss_conf             98806899999699999858-----------------------------------------------------9876999


Q ss_pred             EECCCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCC-CCEEEEEECCCEEEEEECCCCCCCCCCCCCCE
Q ss_conf             97599345301788486675774148876067777686899997289-96499994599899999010554451568738
Q gi|254780182|r  803 VSEKGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVND-NDQIILVSDKGTLIRVPVNEIRIASRATKGVV  881 (910)
Q Consensus       803 vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~-~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~  881 (910)
                      +|.+|+||++++++|...++  .|.++|++.+.   +.++++..+.. +|+|+++|++|+++|++.+++|.+|| ++||+
T Consensus       607 aTk~G~~kr~~l~e~~~~~k--~G~~ai~L~~g---Delv~~~~i~~~~d~I~lvT~~Gk~lrF~~~evr~~gR-gkGVk  680 (745)
T PRK05561        607 ASSAGYGFVVSEEDLVGRNR--AGKAVINLKDG---DKVLAPVPVEGDEDSLAAITQRGRLLVFPLSELPELSR-GKGVK  680 (745)
T ss_pred             EECCCEEEEEEHHHHCCCCC--CCEEEEEECCC---CEEEEEEEECCCCCEEEEEECCCCEEEEEHHHCCCCCC-CCCCC
T ss_conf             97893299978698004462--67188861899---88988899469998899995898289979888777575-46801


Q ss_pred             EEEECCCCEEEEEEEECCCC
Q ss_conf             89808998799999835665
Q gi|254780182|r  882 IFSTAKDERVVSVERIRESE  901 (910)
Q Consensus       882 i~~L~~~D~Vv~va~i~~~e  901 (910)
                      .|+|.++|.|+++..++.++
T Consensus       681 gikLk~~D~Vv~~~vv~~~~  700 (745)
T PRK05561        681 LIELKKEEGLADLAVLPPGD  700 (745)
T ss_pred             EEEECCCCEEEEEEEECCCC
T ss_conf             47668999899999985888


No 21 
>COG0188 GyrA Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair]
Probab=99.72  E-value=1.5e-15  Score=158.12  Aligned_cols=81  Identities=25%  Similarity=0.322  Sum_probs=34.3

Q ss_pred             EEEEECCCCEEEECHHHHHHC--CCCCEEEEEECCCCEEEEEEECCCCC-EEEEEECCCEEEEEEHHHCCCCCCCCCCCE
Q ss_conf             999947991898423686204--77722786615898578889618982-699993698599975876235478665535
Q gi|254780182|r  648 VVFATKHGNVRRNKLSDFIQI--NRSGKIAMKLDSRDEILSVETCTQEN-DILLTTKLGQCVRFPISAIRVFAGRNSVGV  724 (910)
Q Consensus       648 Lvl~Tk~G~VKkt~l~ef~~~--r~~G~~aikLkegD~Li~v~~~~~~~-~Iil~T~~G~~lrF~~~evr~~~GR~a~GV  724 (910)
                      ++++|.+|+.-+.+.+++...  ...|...|+|+++|.++++..+..++ .++.+|.+|...|.+.++.+. ++|+++|+
T Consensus       653 i~~~t~~G~~~~F~~~~v~~~gr~a~Gv~~i~l~~~d~~~~~~~~~~~~~~~l~~t~~g~~kr~~~~~~~~-~~Rg~~G~  731 (804)
T COG0188         653 ILLVTSNGKALRFPESEVREMGRGAKGVKGIKLKEGDKVVSLSVVEDDEAKLLTVTERGYGKRTKISEYPV-TKRGGKGV  731 (804)
T ss_pred             EEEEECCCEEEEEEHHHCCCCCCCCCCCCEEECCCCCEEEEEEECCCCCEEEEEEECCCCEEECCHHHCCC-CCCCCCCE
T ss_conf             89991487378740344221154136864064376575665320147860589984367200041421342-46676641


Q ss_pred             EEEEC
Q ss_conf             76752
Q gi|254780182|r  725 RGISL  729 (910)
Q Consensus       725 kgIkL  729 (910)
                      ..++.
T Consensus       732 ~~~~~  736 (804)
T COG0188         732 ILIKG  736 (804)
T ss_pred             ECCCC
T ss_conf             24545


No 22 
>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=99.52  E-value=4.9e-14  Score=144.68  Aligned_cols=199  Identities=21%  Similarity=0.311  Sum_probs=167.7

Q ss_pred             EEEEEECCC-CEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCE-
Q ss_conf             799994799-189842368620477722786615898578889618982699993698599975876235478665535-
Q gi|254780182|r  647 YVVFATKHG-NVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGV-  724 (910)
Q Consensus       647 ~Lvl~Tk~G-~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GV-  724 (910)
                      +-|.+||.| ++|+++-..|...   -..=++++++|.|+.....+..|+|+++|+.|.+|-.|.-++.-+ -.+-.|- 
T Consensus       499 ~~v~itk~GnY~K~~S~~sf~ss---~~~d~g~~~~d~l~~~~~~nttd~lL~~Ts~g~~In~pvh~La~~-rwkd~g~h  574 (745)
T TIGR01061       499 LYVVITKDGNYIKRTSKRSFASS---KYDDFGLKDDDILFYQTIANTTDKLLIFTSKGNLINLPVHKLADI-RWKDLGEH  574 (745)
T ss_pred             CEEEEEECCCEEHHHHHHHHHHC---CCCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCEEEEEEEECCCC-CHHHHHHH
T ss_conf             40799844763000126676204---731157755334535465212253788761666642130314566-56689987


Q ss_pred             --EEEE-CCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEE
Q ss_conf             --7675-2899869998973366654200000122233333334555444444443332222232001110125686799
Q gi|254780182|r  725 --RGIS-LAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFIL  801 (910)
Q Consensus       725 --kgIk-L~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL  801 (910)
                        +-+. +..++.||.+.+++..+.                                                 ++..++
T Consensus       575 ls~~~~n~~~~E~iv~v~~~~~fdv-------------------------------------------------~~~~L~  605 (745)
T TIGR01061       575 LSNKITNFDENETIVAVEILNEFDV-------------------------------------------------DEAILV  605 (745)
T ss_pred             HCCHHHHHHCCCCEEEEEEECCCCC-------------------------------------------------CHHHHH
T ss_conf             2000110210684899986132257-------------------------------------------------468989


Q ss_pred             EEECCCCEEEEEHHHCCCCCC-CCCCEEEEECCCCCCCCCEEEEEECCC--CCEEEEEECCCEEEEEECCCCCCCCCCCC
Q ss_conf             997599345301788486675-774148876067777686899997289--96499994599899999010554451568
Q gi|254780182|r  802 TVSEKGFGKRTSSYDFRISNR-SGKGIRATDVSKINEIGALVAVFPVND--NDQIILVSDKGTLIRVPVNEIRIASRATK  878 (910)
Q Consensus       802 ~vTe~G~GKRt~~~eyr~q~R-GgkGv~~ik~~~~n~~g~lv~~~~V~~--~DeIlliT~~G~iiR~~v~~I~~~gR~a~  878 (910)
                      +.|.+|..||+.+.+|..+.- --|-+.+|++...   +.||.|+....  ++.|+++|+.|-..+|.++|||..|+-|+
T Consensus       606 l~sklg~vKriel~~l~~~~~y~sK~~~~~~L~D~---d~li~a~~~~~Gh~~~i~lvS~~gy~l~F~~~Ei~~~~~~A~  682 (745)
T TIGR01061       606 LASKLGMVKRIELTELDIKRNYRSKAILILKLKDE---DELISAFLQKKGHDKLIILVSKLGYALLFLVEEINVVGAKAA  682 (745)
T ss_pred             HHHHCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC---CCEEEEEEECCCCCCEEEEEEECCCEEEECCEEECCCCCCCC
T ss_conf             98755874787603247786510122332111789---543899984188844189997368357730203323144667


Q ss_pred             CCEEEEECCCCEEEEEEEECCCC
Q ss_conf             73889808998799999835665
Q gi|254780182|r  879 GVVIFSTAKDERVVSVERIRESE  901 (910)
Q Consensus       879 GV~i~~L~~~D~Vv~va~i~~~e  901 (910)
                      ||+.|+|+++|.|.++...+..+
T Consensus       683 GvK~mkLK~~D~v~~~~i~~~~~  705 (745)
T TIGR01061       683 GVKGMKLKEDDEVKSGLILEANE  705 (745)
T ss_pred             CEEEEECCCCCEEEEEEEECCCC
T ss_conf             31133057676389999982799


No 23 
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit; InterPro: IPR005742   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=98.71  E-value=1.1e-06  Score=78.88  Aligned_cols=186  Identities=19%  Similarity=0.307  Sum_probs=140.1

Q ss_pred             EEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEE
Q ss_conf             99994799189842368620477722786615898578889618982699993698599975876235478665535767
Q gi|254780182|r  648 VVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGI  727 (910)
Q Consensus       648 Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgI  727 (910)
                      -+.+++.|-|.-....+..      ...++-|+||.-........++.|+++++.|+.--.....++  +||+..|--.+
T Consensus       508 Tii~S~MGWVRs~KGH~~D------~~~l~YK~GD~~~~~~~~~~~~~v~~i~S~GR~y~l~~~~l~--~a~g~G~Pl~~  579 (747)
T TIGR01062       508 TIILSKMGWVRSAKGHDID------LSTLKYKAGDSEKAIIEGKSNQKVVFIDSTGRSYALDPLNLP--SARGQGEPLTG  579 (747)
T ss_pred             EEEECCCCCEEECCCCCCC------CCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEEECCCCCC--CCCCCCCCEEE
T ss_conf             7998277735504665667------143541368612334551277517999728852663112043--45677872268


Q ss_pred             EC--CCC-CEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEE
Q ss_conf             52--899-869998973366654200000122233333334555444444443332222232001110125686799997
Q gi|254780182|r  728 SL--AKG-DQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVS  804 (910)
Q Consensus       728 kL--~~~-D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vT  804 (910)
                      ||  ..| ..|-.+. +                                                    ..+++.+|+.|
T Consensus       580 KL~l~~Gn~~i~~~l-~----------------------------------------------------~~~~Q~LL~AS  606 (747)
T TIGR01062       580 KLLLPIGNATIENIL-M----------------------------------------------------ESENQKLLLAS  606 (747)
T ss_pred             EEECCCCCCCEEEEE-E----------------------------------------------------ECCCCCEEEEC
T ss_conf             873268862310777-6----------------------------------------------------35885321000


Q ss_pred             CCCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCC-CEEEEEECCCEEEEEECCCCCCCCCCCCCCEEE
Q ss_conf             5993453017884866757741488760677776868999972899-649999459989999901055445156873889
Q gi|254780182|r  805 EKGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDN-DQIILVSDKGTLIRVPVNEIRIASRATKGVVIF  883 (910)
Q Consensus       805 e~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~-DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~  883 (910)
                      +-|||-.+..++.=-++|+||-+.++.  + |  ..++.+.+|+++ +-|+.||+.|+++-+++++||.+++. +|++++
T Consensus       607 ~~G~GF~~~~~~liA~~k~GK~l~~lP--E-~--~~~~~p~~~~~~s~~~~aI~~a~R~L~F~~~~lP~l~KG-~G~~~~  680 (747)
T TIGR01062       607 DAGYGFLVKFNDLIARNKAGKALINLP--E-N--ASVLAPLVVNDDSDLIVAITEAGRLLVFPIDDLPELSKG-KGNKLI  680 (747)
T ss_pred             CCCCCEEEECHHHHHHCHHCHHHCCCC--C-C--CEEECCEEECCCCCEEEEECCCCEEEEECHHHCCCCCCC-CCCEEE
T ss_conf             168624740043333110040200178--8-8--611044342376102444113670687421117763478-730577


Q ss_pred             EECC------CCEEEEEEEECCC
Q ss_conf             8089------9879999983566
Q gi|254780182|r  884 STAK------DERVVSVERIRES  900 (910)
Q Consensus       884 ~L~~------~D~Vv~va~i~~~  900 (910)
                      +...      .|.+..+..++..
T Consensus       681 ~~~~a~A~~~~~~L~~l~~~~~Q  703 (747)
T TIGR01062       681 RIPAANAKDREELLLDLKILNKQ  703 (747)
T ss_pred             EECCHHHCCCCCCCEEEEEECCC
T ss_conf             50541001200010123453577


No 24 
>PRK09631 DNA topoisomerase IV subunit A; Provisional
Probab=98.06  E-value=0.0034  Score=47.68  Aligned_cols=68  Identities=22%  Similarity=0.173  Sum_probs=39.6

Q ss_pred             CCCCEEEECHHHHHH--CCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEE
Q ss_conf             799189842368620--4777227866158985788896189826999936985999758762354786655357
Q gi|254780182|r  653 KHGNVRRNKLSDFIQ--INRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVR  725 (910)
Q Consensus       653 k~G~VKkt~l~ef~~--~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVk  725 (910)
                      .++.+||++++.|..  .+..|.+.+.|++||.+..   |+.-|+|++.| +|........+- ...|++-.-|.
T Consensus       458 d~i~aKrVa~~n~Kly~nr~~GFiGtslKkdDfV~~---CSd~DdILvF~-dG~ykV~kV~~K-~Fvgk~i~~v~  527 (626)
T PRK09631        458 KSKNVREIATKNMKVYLNLETGFVGTSLIDGEFIGN---ASYYDKILIFK-DGSYVLKNIEDK-TFIDKKNVCVL  527 (626)
T ss_pred             CCEEEEEEECCCCEEEECCCCCEEEECCCCCCEEEE---CCCCCEEEEEE-CCEEEEEECCCC-CEECCCCEEEE
T ss_conf             444369957023325665888556103567845673---35665399998-985999985776-05468837999


No 25 
>pfam03989 DNA_gyraseA_C DNA gyrase C-terminal domain, beta-propeller. This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure. This region has been shown to bind DNA non-specifically and may stabilize the DNA-topoisomerase complex.
Probab=97.96  E-value=3.3e-05  Score=65.71  Aligned_cols=47  Identities=32%  Similarity=0.555  Sum_probs=21.2

Q ss_pred             CEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCCCEEEEEEEE
Q ss_conf             64999945998999990105544515687388980899879999983
Q gi|254780182|r  851 DQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKDERVVSVERI  897 (910)
Q Consensus       851 DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~D~Vv~va~i  897 (910)
                      |+++++|+.|.++|++++++|.++|.++||++|+|.++|+|+++..+
T Consensus         2 ~~lll~T~~G~~~r~~~~~~~~~~r~~~Gv~~~~l~~~d~v~~~~~~   48 (50)
T pfam03989         2 DDLLLITSKGYVKRTPLSEFPEQGRGAKGVKAINLKEGDKVVSVLVV   48 (50)
T ss_pred             CEEEEEECCCEEEEEECHHCCCCCCCCCCEEEEECCCCCEEEEEEEC
T ss_conf             78999908998999893154546876878797887999999999991


No 26 
>pfam03989 DNA_gyraseA_C DNA gyrase C-terminal domain, beta-propeller. This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure. This region has been shown to bind DNA non-specifically and may stabilize the DNA-topoisomerase complex.
Probab=97.86  E-value=6.2e-05  Score=63.21  Aligned_cols=48  Identities=42%  Similarity=0.694  Sum_probs=34.8

Q ss_pred             CCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCCEEEEEEEE
Q ss_conf             8269999369859997587623547866553576752899869998973
Q gi|254780182|r  693 ENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGDQVISMAIV  741 (910)
Q Consensus       693 ~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi  741 (910)
                      +++++++|+.|++.||+.+++++ +||+++||++|+|+++|+|+++.++
T Consensus         1 ~~~lll~T~~G~~~r~~~~~~~~-~~r~~~Gv~~~~l~~~d~v~~~~~~   48 (50)
T pfam03989         1 EDDLLLITSKGYVKRTPLSEFPE-QGRGAKGVKAINLKEGDKVVSVLVV   48 (50)
T ss_pred             CCEEEEEECCCEEEEEECHHCCC-CCCCCCCEEEEECCCCCEEEEEEEC
T ss_conf             97899990899899989315454-6876878797887999999999991


No 27 
>PRK09630 DNA topoisomerase IV subunit A; Provisional
Probab=97.56  E-value=0.0059  Score=45.50  Aligned_cols=112  Identities=12%  Similarity=-0.028  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHH
Q ss_conf             999999999999999999999999888778999999874-------0699999986189978987877631269788999
Q gi|254780182|r  357 ILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVA-------NLDEVVRIIRFSPNPETARRELMQRSWNASDIKD  429 (910)
Q Consensus       357 iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~-------nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~  429 (910)
                      -|.+|++|+.+.+++..++++...++|+.- +-+...++       .+|.|+++|+..++...++......         
T Consensus       308 ~l~eiL~~~~~~~~~~lrr~l~~~~~~~~r-~~~~k~Le~l~I~~~~~d~I~eiI~~i~~~~~~ed~~~~l---------  377 (479)
T PRK09630        308 SISEILKLHTEALQGYLKKELLILQDSLTR-EHYHKTLEYIFIKHKLYDTVREMLSKRKTKPSASDLHNAV---------  377 (479)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH---------
T ss_conf             689999999998755434668999899999-9999888899998778999999999885389899999999---------


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q ss_conf             99740221112223445236999999999878999988879999-998999999999887530
Q gi|254780182|r  430 LIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDI-RNELNSLGIEIKECLDIL  491 (910)
Q Consensus       430 ~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl-~~E~~eL~~~I~~l~~IL  491 (910)
                                   ......|+..|+++|++|++++|+.|+..+| .-|..++.++++++++-+
T Consensus       378 -------------~~~~~~~~~~~~~~i~~q~~~~L~~l~l~kL~~Le~~k~~~El~~l~~~i  427 (479)
T PRK09630        378 -------------LHALEPFLHTLPTAPDKQATSQLASLTIKKILCFNENAYTKELAAIEKKQ  427 (479)
T ss_pred             -------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -------------98765667877543389999999998999875133999999999999999


No 28 
>KOG1240 consensus
Probab=96.68  E-value=0.095  Score=34.72  Aligned_cols=153  Identities=18%  Similarity=0.242  Sum_probs=102.9

Q ss_pred             CEEEEEECCCCEEEECHHHHHHCCCCCEEEEEEC-CCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCE
Q ss_conf             1799994799189842368620477722786615-898578889618982699993698599975876235478665535
Q gi|254780182|r  646 LYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLD-SRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGV  724 (910)
Q Consensus       646 ~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLk-egD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GV  724 (910)
                      .|++-++.+|.||-..+.+...-...-.--.+.. ++-..-.+..|...+.+++.|++|.+..+.++.... .-+.+.-+
T Consensus      1062 s~FvsgS~DGtVKvW~~~k~~~~~~s~rS~ltys~~~sr~~~vt~~~~~~~~Av~t~DG~v~~~~id~~~~-~~~~~~~~ 1140 (1431)
T KOG1240        1062 SLFVSGSDDGTVKVWNLRKLEGEGGSARSELTYSPEGSRVEKVTMCGNGDQFAVSTKDGSVRVLRIDHYNV-SKRVATQV 1140 (1431)
T ss_pred             CEEEEECCCCEEEEEEEHHHHCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEECCCCEEEEEECCCCCC-CCCEEEEE
T ss_conf             65797058865898651112167640355688712688468998516887688972787289997254343-31002333


Q ss_pred             EEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEE
Q ss_conf             76752899869998973366654200000122233333334555444444443332222232001110125686799997
Q gi|254780182|r  725 RGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVS  804 (910)
Q Consensus       725 kgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vT  804 (910)
                      +-.++++.+.||+|-.......                                                  ...++.+|
T Consensus      1141 ri~n~~~~g~vv~m~a~~~~~~--------------------------------------------------S~~lvy~T 1170 (1431)
T KOG1240        1141 RIPNLKKDGVVVSMHAFTAIVQ--------------------------------------------------SHVLVYAT 1170 (1431)
T ss_pred             ECCCCCCCCCEEEEECCCCCCC--------------------------------------------------CEEEEEEE
T ss_conf             1356657883688633420036--------------------------------------------------52699997


Q ss_pred             CCCCEE----EEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCC-CEEEEEECCCEEE
Q ss_conf             599345----3017884866757741488760677776868999972899-6499994599899
Q gi|254780182|r  805 EKGFGK----RTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDN-DQIILVSDKGTLI  863 (910)
Q Consensus       805 e~G~GK----Rt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~-DeIlliT~~G~ii  863 (910)
                      .+|-+-    |+..+-.+.|+           ..  +.| +|...++++. ..+++-|++|+++
T Consensus      1171 ~~~~iv~~D~r~~~~~w~lk~-----------~~--~hG-~vTSi~idp~~~WlviGts~G~l~ 1220 (1431)
T KOG1240        1171 DLSRIVSWDTRMRHDAWRLKN-----------QL--RHG-LVTSIVIDPWCNWLVIGTSRGQLV 1220 (1431)
T ss_pred             ECCCEEEECCHHHHHHHHHHC-----------CC--CCC-CEEEEEECCCCEEEEEECCCCEEE
T ss_conf             126268841312566776405-----------74--556-046798558761899965785599


No 29 
>KOG3863 consensus
Probab=87.30  E-value=2.4  Score=22.21  Aligned_cols=64  Identities=22%  Similarity=0.270  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH----------
Q ss_conf             7406999999861899789878776312697889999974022111222344523699999999987899----------
Q gi|254780182|r  394 VANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLA----------  463 (910)
Q Consensus       394 l~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~----------  463 (910)
                      --.-|+||.+.+.+      =..++++                          |+||+.|-.-|=|.|=|          
T Consensus       458 PF~vd~IinLp~~d------Fne~ls~--------------------------~~lte~QLslIrDIRRRgKNkvAAQnC  505 (604)
T KOG3863         458 PFSVDEIINLPVDD------FNEMLSK--------------------------YKLTEEQLSLIRDIRRRGKNKVAAQNC  505 (604)
T ss_pred             CCCHHHHCCCCHHH------HHHHHHH--------------------------CCCCHHHHHHHHCCCCCCCCCHHCCCH
T ss_conf             87667653786889------9999985--------------------------026898877765021045651001320


Q ss_pred             HHHHHHH-HHHHHHHHHHHHHHHHHHH
Q ss_conf             9988879-9999989999999998875
Q gi|254780182|r  464 RLTGLGR-DDIRNELNSLGIEIKECLD  489 (910)
Q Consensus       464 rLt~LE~-~kl~~E~~eL~~~I~~l~~  489 (910)
                      |=.+|+. ..|+.|...|.++.+.|.+
T Consensus       506 RKRKLd~I~nLE~ev~~l~~eKeqLl~  532 (604)
T KOG3863         506 RKRKLDCILNLEDEVEKLQKEKEQLLR  532 (604)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             356778999888999988888898899


No 30 
>KOG1920 consensus
Probab=86.96  E-value=2.5  Score=22.06  Aligned_cols=16  Identities=31%  Similarity=0.503  Sum_probs=8.2

Q ss_pred             CEEEEEEECCCCCHHHHH
Q ss_conf             557999947988778999
Q gi|254780182|r  307 GYRVVIELKRGASADVIL  324 (910)
Q Consensus       307 giRivielKr~~~~~~vl  324 (910)
                      |-+||=-++.+  +.+||
T Consensus       649 GsklVa~~~~k--a~VvL  664 (1265)
T KOG1920         649 GSKLVAVVPQK--AAVVL  664 (1265)
T ss_pred             CCEEEEECCCH--HHHHH
T ss_conf             05578862412--56867


No 31 
>TIGR02895 spore_sigI RNA polymerase sigma-I factor; InterPro: IPR014244   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This entry represents the transcription factor Sigma-I. This protein is found in endospore-forming species in the Firmicutes lineage of bacteria, such as Bacillus subtilis, but is not universally present among such species. Sigma-I was shown to be induced by heat shock  in B. subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=85.67  E-value=2.5  Score=21.93  Aligned_cols=100  Identities=25%  Similarity=0.300  Sum_probs=81.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCC
Q ss_conf             99999999999999999999988877899999987406999999861899789878776312697889999974022111
Q gi|254780182|r  360 AFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSY  439 (910)
Q Consensus       360 ~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~  439 (910)
                      .|+.|-.-||+||                           ||+-||.-....++                          
T Consensus        64 sFL~FA~l~IkRr---------------------------~IDy~R~n~k~~~~--------------------------   90 (225)
T TIGR02895        64 SFLSFAKLIIKRR---------------------------VIDYIRKNQKYKNL--------------------------   90 (225)
T ss_pred             HHHHHHHHHHHHH---------------------------HHHHHHHHHHHHHC--------------------------
T ss_conf             1699999988999---------------------------88888741112211--------------------------


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCE
Q ss_conf             22234452369999999998789999888799999989999999998875304989999999998999998405688331
Q gi|254780182|r  440 TIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTR  519 (910)
Q Consensus       440 ~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~  519 (910)
                       ....+.|.=||.|++--|+|.+.    +|.-+=+-|...-+.+|-+|++.|.    +|++=-.||-+.-=||-|-|.+.
T Consensus        91 -~~l~e~y~n~E~~~~~~~~~~~~----~e~y~~~i~~~~RrlEILey~~~L~----~f~I~f~eLv~~SPKH~d~R~~~  161 (225)
T TIGR02895        91 -VYLDEDYDNSEENDENSLEIKVS----LEEYKNEIENENRRLEILEYKKLLK----QFGIEFVELVKVSPKHRDARKKA  161 (225)
T ss_pred             -CCCCCCCCCHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCHHHHHCCCCCHHHHHHHH
T ss_conf             -67677656403577548999999----9999987588866899999999998----73870768741077768899999


Q ss_pred             EE
Q ss_conf             00
Q gi|254780182|r  520 IV  521 (910)
Q Consensus       520 I~  521 (910)
                      |.
T Consensus       162 ~~  163 (225)
T TIGR02895       162 IK  163 (225)
T ss_pred             HH
T ss_conf             99


No 32 
>pfam11197 DUF2835 Protein of unknown function (DUF2835). This is a bacterial family of uncharacterized proteins. One member of this family is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
Probab=84.82  E-value=2.9  Score=21.37  Aligned_cols=45  Identities=18%  Similarity=0.522  Sum_probs=35.2

Q ss_pred             CCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEE---EECCCCCEEEEE
Q ss_conf             98269999369859997587623547866553576---752899869998
Q gi|254780182|r  692 QENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRG---ISLAKGDQVISM  738 (910)
Q Consensus       692 ~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkg---IkL~~~D~Vv~~  738 (910)
                      ..+.|.+.|.+|+-++||.+.+||.-  +..||+|   |.+.++-+.++.
T Consensus        19 ~a~~V~v~~~~Gr~l~lPa~~lrpFv--t~~GI~G~F~l~~d~~~kf~sL   66 (68)
T pfam11197        19 AASKVVVRSRDGRRLQLPARRLRPFL--THDGIRGRFRLEFDDNGKFVSL   66 (68)
T ss_pred             CCCEEEEEECCCCEEEEEHHHCCCCC--CCCCCEEEEEEEECCCCCEEEE
T ss_conf             46589999079949997679875305--6788459999999899989872


No 33 
>KOG4212 consensus
Probab=82.44  E-value=1.9  Score=22.97  Aligned_cols=63  Identities=30%  Similarity=0.472  Sum_probs=45.6

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             9999246443528999999999987166--501445873037465579999479887789999999761
Q gi|254780182|r  265 QIVVTEIPYQVNKAAMLEKIAELVREKR--IVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYT  331 (910)
Q Consensus       265 ~ivItEiPY~vnk~~lie~Ia~lv~~~k--i~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T  331 (910)
                      ...||.|||.+.   | ..+.+||++|-  ++-+.=+-|+|.|--=.-|+|.|-..+.++-+..|-||.
T Consensus        46 ~vfItNIpyd~r---W-qdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~  110 (608)
T KOG4212          46 SVFITNIPYDYR---W-QDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYE  110 (608)
T ss_pred             EEEEECCCCHHH---H-HHHHHHHHHHCCCEEEEEEECCCCCCCCCCEEEEEECHHHHHHHHHHHHHCC
T ss_conf             478865753211---3-7699999974473586652013478857734798507778999999864434


No 34 
>pfam04201 TPD52 Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other.
Probab=81.25  E-value=3.1  Score=21.12  Aligned_cols=49  Identities=22%  Similarity=0.407  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             98887999999899999999988753049899999999989999984056883310
Q gi|254780182|r  465 LTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI  520 (910)
Q Consensus       465 Lt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I  520 (910)
                      |+--|++.++.|+..+.++|..|+..|+.+.+...       +||.+.|.-.-.+|
T Consensus        26 lseee~eel~~EL~kvEeEI~tLrqvLaaKer~~~-------elKrkLGit~~~eL   74 (162)
T pfam04201        26 LSEAEKEELRTELAKLEEEISTLRQVLAAKEKHLA-------ELKRKLGLTPLSEL   74 (162)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHCCCHHHHH
T ss_conf             78999999999999999999999999999999999-------99998687569999


No 35 
>pfam05133 Phage_prot_Gp6 Phage portal protein, SPP1 Gp6-like. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, Gp6 participates in the procapsid assembly reaction. This family also includes family Phage_min_cap, pfam05126.
Probab=79.96  E-value=4.3  Score=19.84  Aligned_cols=12  Identities=42%  Similarity=0.495  Sum_probs=7.4

Q ss_pred             CCCCCCHHHHHH
Q ss_conf             769720135789
Q gi|254780182|r  121 DGDPPAAERYTE  132 (910)
Q Consensus       121 dgd~~AA~RYte  132 (910)
                      ++.++|+.||..
T Consensus       140 ~~~~~~~vr~~~  151 (435)
T pfam05133       140 DRELAAAVRYYT  151 (435)
T ss_pred             CCCEEEEEEEEE
T ss_conf             876359999999


No 36 
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=77.10  E-value=0.67  Score=27.14  Aligned_cols=14  Identities=14%  Similarity=-0.028  Sum_probs=6.0

Q ss_pred             CHHHHHHHHHHHCC
Q ss_conf             04789999997122
Q gi|254780182|r   89 GNAAIYDALARMAQ  102 (910)
Q Consensus        89 Gd~siy~a~v~maq  102 (910)
                      |..|+|.+-+..+|
T Consensus       162 ~~~s~~~~ni~~~~  175 (749)
T COG5207         162 GPSSIEMGNIGGLK  175 (749)
T ss_pred             CCCCCCCCCCCCCE
T ss_conf             99863013557732


No 37 
>KOG4010 consensus
Probab=76.56  E-value=5.3  Score=19.07  Aligned_cols=43  Identities=23%  Similarity=0.386  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             9998887999999899999999988753049899999999989
Q gi|254780182|r  463 ARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQEL  505 (910)
Q Consensus       463 ~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL  505 (910)
                      --|+--|.+.|+.|+..+.++|..|+..|+.+++-..-||.-|
T Consensus        39 ~~LSe~Ekeelr~EL~kvEeEI~TLrqVLaAKerH~~ELKRKL   81 (208)
T KOG4010          39 EALSEEEKEELRTELAKVEEEIVTLRQVLAAKERHAAELKRKL   81 (208)
T ss_pred             HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6506888999999999999999999999999888899999986


No 38 
>pfam12395 DUF3658 Protein of unknown function. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam08874. There are two completely conserved residues (D and R) that may be functionally important.
Probab=75.61  E-value=1.5  Score=24.08  Aligned_cols=53  Identities=26%  Similarity=0.354  Sum_probs=31.3

Q ss_pred             CCCCEEEEHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             99981134042556643668-8704789999997122011156131478870887769720135789
Q gi|254780182|r   67 WNKKYVKCARISGEVMGKYH-PHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTE  132 (910)
Q Consensus        67 ~~~~~~K~a~ivg~v~gkyH-PHGd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte  132 (910)
                      ....|.|+||+||+|||++. +-||.=+.=-+=-|+           -||-|=-. |++ .+||+-+
T Consensus        57 ~~~~~~~a~rvIg~v~g~~~~~v~D~fl~~Rir~Li-----------~~G~le~~-G~~-~~m~~~~  110 (111)
T pfam12395        57 ATDEFQKAARVVGEVMGHLEQLVGDTFLEYRIRELI-----------KQGVLELK-GDL-KSMRDYS  110 (111)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH-----------HCCCEEEE-CCC-CHHHCCC
T ss_conf             835445999999999986677777899999999999-----------88988996-584-3523021


No 39 
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=72.01  E-value=6.6  Score=18.20  Aligned_cols=130  Identities=17%  Similarity=0.041  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE-ECCCCCCCCCCCCCCCCEEEEEECCC-EE
Q ss_conf             99999899999999988753049899999999989999984056883310-01343453010145678189990797-05
Q gi|254780182|r  471 DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI-VEGLLDMEDEDCIVREDMVVTVSHLG-YV  548 (910)
Q Consensus       471 ~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I-~~~~~~i~~EdlI~~E~vvV~lS~~G-yI  548 (910)
                      +++.+++.+|..++.+|+.-+..-+..+.-+++|+..+++.-..=|..-. +..     ..+.+.+..++|-.|... |+
T Consensus         5 ~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~l~~~~~~l~~e~~~l~~~p~~vg~-----~~~~~~~~~~iv~~~~g~~~~   79 (390)
T PRK03992          5 EKLDDREEQLESRNEELEEQLRDLEAENERLERELERLKSELEKLRTPPLIVAT-----VLEVLDDGRVVVKSSTGPQFV   79 (390)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE-----EEEEECCCEEEEEECCCCEEE
T ss_conf             999999999999999999999999999999999999999999985489948999-----999837974999978998799


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCC
Q ss_conf             23310000023345652110001464101011332377739999548939998200043224445655
Q gi|254780182|r  549 KRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGK  616 (910)
Q Consensus       549 Kr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~  616 (910)
                      =++...           +.--.++.++.|.---.+.+--.+|=-....+|+.+.+-+-|..+|..-|-
T Consensus        80 v~~~~~-----------~~~~~l~pg~~V~l~~~~~~i~~~l~~~~d~~v~~m~v~e~P~v~~~dIGG  136 (390)
T PRK03992         80 VTVSSF-----------VDRDKLKPGARVALNQQTLAIVEVLPSEKDPRVRAMEVIESPDVTYEDIGG  136 (390)
T ss_pred             EECCCC-----------CCHHHCCCCCEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHCC
T ss_conf             965787-----------688887999989985353030564688878621104214799998466149


No 40 
>pfam10977 DUF2797 Protein of unknown function (DUF2797). This family of proteins has no known function.
Probab=71.60  E-value=4.4  Score=19.81  Aligned_cols=25  Identities=24%  Similarity=-0.064  Sum_probs=11.1

Q ss_pred             EEECCCCEEEEECCCCCCCCCCCCCC
Q ss_conf             99548939998200043224445655
Q gi|254780182|r  591 FFSSLGFVYKEKVWRLPIGSPQARGK  616 (910)
Q Consensus       591 fFTs~Gkvy~l~v~~IP~~sr~skG~  616 (910)
                      .-||.=||=..+..++| ..|-..|-
T Consensus        76 A~ss~~KVGITR~~q~p-tRWiDQGA  100 (233)
T pfam10977        76 ANSSGVKVGITRKTQLP-TRWIDQGA  100 (233)
T ss_pred             ECCCCCEEEEECCCCCC-CCHHHCCC
T ss_conf             84898478787789986-45566181


No 41 
>pfam03982 DAGAT Diacylglycerol acyltransferase. The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT).
Probab=71.54  E-value=1  Score=25.53  Aligned_cols=67  Identities=22%  Similarity=0.433  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCHHHHHHHH-------HHH----------HCCCCCCCCEEEEHHHHHHHHCCCCCCCHHH
Q ss_conf             87779988631375400089736789999-------999----------8789999981134042556643668870478
Q gi|254780182|r   30 LTYAINVILGRAIPDLRDGLKPVHRRILF-------GMM----------QMGVEWNKKYVKCARISGEVMGKYHPHGNAA   92 (910)
Q Consensus        30 l~Ya~svI~~RAlPd~rDGlKpv~Rrily-------~m~----------~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~s   92 (910)
                      +-|+.....+|.-|.- .|     ||.-|       --+          .-.|.|++.|         +.| |||||=.+
T Consensus        13 ~~Y~~w~~~d~~tp~~-gg-----r~~~w~R~~~iwk~~~~YFPi~Lvkt~~L~p~~nY---------ifg-~hPHGil~   76 (297)
T pfam03982        13 VLYALWLFYDWNSPKR-GG-----YRSNWARNWRIWKWFANYFPVKLHKTAELPPNRNY---------LFG-YHPHGILS   76 (297)
T ss_pred             HHHHHHHHEECCCCCC-CC-----CCCHHEECCHHHHHHHHHCCCEEEECCCCCCCCCE---------EEE-ECCCCEEC
T ss_conf             9999774046788889-99-----71511013777887875188147875668998454---------888-76851032


Q ss_pred             HHHHHHHHCCC---HHCCCCCCCC
Q ss_conf             99999971220---1115613147
Q gi|254780182|r   93 IYDALARMAQD---WSLRLLLIEG  113 (910)
Q Consensus        93 iy~a~v~maq~---~~~r~plidg  113 (910)
                      + .|.+.+|.+   |+--+|-+..
T Consensus        77 ~-Ga~~~f~t~~~~f~~lfPgi~~   99 (297)
T pfam03982        77 V-GAFSNFSTNATGFMDKFPGIRP   99 (297)
T ss_pred             C-CHHEEECCCCCCCHHHCCCCCC
T ss_conf             4-2110323455585756799987


No 42 
>TIGR02515 IV_pilus_PilQ type IV pilus secretin PilQ; InterPro: IPR013355    A number of proteins homologous to PilQ are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also referred to as the main terminal branch of the general secretion pathway). Members of this family include PilQ itself, which is a component of the type IV pilus structure, from a number of species. In Haemophilus influenzae, the member of this family is associated with the uptake of exogenous DNA, rather than with formation of a type IV pilus - the surface structure required for this may be considered an unusual, incomplete type IV pilus structure.; GO: 0009297 pilus biogenesis, 0009306 protein secretion.
Probab=70.30  E-value=5.5  Score=18.95  Aligned_cols=36  Identities=17%  Similarity=0.408  Sum_probs=23.5

Q ss_pred             CCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEE
Q ss_conf             6757741488760677776868999972899649999459989999
Q gi|254780182|r  820 SNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRV  865 (910)
Q Consensus       820 q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~  865 (910)
                      ..-|+.|+.+|+..      .+-.-..|++++-+.|    |-++..
T Consensus       385 ~~~a~~~~~~I~k~------ei~T~VlV~nGeTvVi----GGIY~~  420 (464)
T TIGR02515       385 VSQAGGGVPAIDKR------EINTQVLVKNGETVVI----GGIYEQ  420 (464)
T ss_pred             CCCCCCCCCCEEEE------EEEEEEEEECCCEEEE----EEEEEE
T ss_conf             34678701504402------6778999725888998----128985


No 43 
>TIGR00909 2A0306 amino acid transporter; InterPro: IPR004758 Amino acid permeases are integral membrane proteins involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related , , . These proteins seem to contain up to 12 transmembrane segments. The best conserved region in this family is located in the second transmembrane segment.   Some proteins in this group are involved in the transport of the cationic amino acids (arginine,lysine and ornithine)..
Probab=69.38  E-value=4.1  Score=20.07  Aligned_cols=35  Identities=26%  Similarity=0.354  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf             67899999998789999981134042556643668870478999999
Q gi|254780182|r   52 VHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALA   98 (910)
Q Consensus        52 v~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v   98 (910)
                      -|=|+||||.+-|+-|.            .+.|-||.=|+.-|.+++
T Consensus       316 g~~RvlFAmSRDGllP~------------slSkvH~k~~tP~~~~~~  350 (451)
T TIGR00909       316 GTSRVLFAMSRDGLLPK------------SLSKVHPKTKTPHVSILI  350 (451)
T ss_pred             HHHHHHHHHHHCCCCCC------------HHHHHCCCCCCCCHHHHH
T ss_conf             89999999986177530------------376323446875048999


No 44 
>cd04793 LanC LanC is the cyclase enzyme of the lanthionine synthetase. Lanthinoine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as precursor peptides and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans) in addition to  2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These unusual amino acids are introduced by the dehydration of serine and threonine residues, followed by thioether formation via addition of cysteine thiols, catalysed by LanB and LanC or LanM. LanC, the cyclase component, is a zinc metalloprotein, whose bound metal has been proposed to activate the thiol substrate for nucleophilic addition.
Probab=68.40  E-value=7.7  Score=17.61  Aligned_cols=70  Identities=21%  Similarity=0.281  Sum_probs=35.0

Q ss_pred             HHCCCCCEEEHHHHCCCC--CCHHHHHHHHHHHHHCCCCCH------HHHHHHCCCCCCCCC----CCCCCHHHHH----
Q ss_conf             101676101013317898--547899999988761877688------888863458668874----4344758899----
Q gi|254780182|r  175 LVNGGGGIAVGMATNIPT--HNLGEVVDGCVAVIDNPDIDL------DALMEIIRGPDFPTG----AVILGRTGIK----  238 (910)
Q Consensus       175 L~nG~~GIAvGmaTnipp--HNl~Ev~~a~~~~i~~p~~~~------~eL~~~i~GPDFPTG----G~I~~~~~i~----  238 (910)
                      +++|.+||+.-+-....+  +-+..+.+.+..+.+.-....      +....-..-+.||.|    |.-+|-.|+.    
T Consensus       103 ~i~G~sGi~~yLL~~~~~~~~~~~~i~~~L~~l~~~~~~~~~~~~~~~~~~~~~~~~~~p~G~~nlG~AHGiaGil~~La  182 (382)
T cd04793         103 VISGLSGIGRYLLLRHEPDSELLREILDYLVYLTEPLNQDITLYIWSENQPSETESKEFPEGHINLGLAHGIAGPLALLA  182 (382)
T ss_pred             CCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             12778999999985046781689999999999998773268777782013671011117777756761054899999999


Q ss_pred             HHHHHC
Q ss_conf             998701
Q gi|254780182|r  239 NAYATG  244 (910)
Q Consensus       239 ~~y~tG  244 (910)
                      .+|+.|
T Consensus       183 la~~~g  188 (382)
T cd04793         183 LAKERG  188 (382)
T ss_pred             HHHHHC
T ss_conf             999846


No 45 
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=67.27  E-value=8.1  Score=17.43  Aligned_cols=46  Identities=22%  Similarity=0.304  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             799999989999999998875304---9899999999989999984056
Q gi|254780182|r  469 GRDDIRNELNSLGIEIKECLDILS---SRSRLLGIIKQELLSVKDELDT  514 (910)
Q Consensus       469 E~~kl~~E~~eL~~~I~~l~~IL~---s~~~l~~iI~~EL~eik~kygd  514 (910)
                      ++.....+|+.+.+.|++-+.||.   ++..+.+.+++||.+++++-.+
T Consensus        48 ~i~~~~~~~~~~~~~~~~A~~~l~E~~~D~El~elak~El~~l~~~~~~   96 (373)
T TIGR00019        48 EIVDKYEEYKKAQEDLKEAKELLEEKGDDKELRELAKEELEELEKEIEE   96 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999999974258865899999999999988888


No 46 
>cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h
Probab=63.90  E-value=6.8  Score=18.10  Aligned_cols=55  Identities=27%  Similarity=0.300  Sum_probs=43.6

Q ss_pred             HHCCCHHCCCCCCCCCCCCCCCCCCCCCHHH---HHHHHHHHHHHHHHHHCCCCCCCCEECC
Q ss_conf             7122011156131478870887769720135---7899978999999863076840533068
Q gi|254780182|r   99 RMAQDWSLRLLLIEGQGNFGSVDGDPPAAER---YTECRLQKAAHFLLDDLGKDTVDFRPNY  157 (910)
Q Consensus        99 ~maq~~~~r~plidg~GnfGs~dgd~~AA~R---Yte~rl~~~~~~~l~~i~~~tv~~~~n~  157 (910)
                      .-||+|++-|+++.+..+-+++|-  ..+|.   ||..+|-+.|++.+..|.-.-+  -++|
T Consensus       149 mWaQ~W~ni~dl~~P~p~~~~~Dv--t~~m~~q~~t~~~mf~~ae~FF~SLGl~~m--p~~F  206 (477)
T cd06461         149 MWAQSWSNIYDLVKPYPGKPLLDV--TDAMVEQGYTAKRMFKEAEEFFTSLGLPPM--PPSF  206 (477)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCC--CHHHHHCCCCHHHHHHHHHHHHHHCCCCCC--CHHH
T ss_conf             665436654201357999888881--599998599899999999999996799769--9778


No 47 
>KOG2264 consensus
Probab=62.87  E-value=9.5  Score=16.79  Aligned_cols=46  Identities=20%  Similarity=0.350  Sum_probs=21.1

Q ss_pred             HHHHHHCCCCCCCCCCC---CCC--HH----HHHHHHHHCCCEEEEEEEEEEEECC
Q ss_conf             88886345866887443---447--58----8999987012038999988654336
Q gi|254780182|r  214 DALMEIIRGPDFPTGAV---ILG--RT----GIKNAYATGRGSIVIRGVSHIEKTS  260 (910)
Q Consensus       214 ~eL~~~i~GPDFPTGG~---I~~--~~----~i~~~y~tGrG~i~iR~k~~ie~~~  260 (910)
                      .||-+.--=|-+-|.|.   +.+  +.    .+.--+.||| +|.+.+...-++..
T Consensus       256 ~eleklyslp~w~~dg~Nhvl~Nl~r~s~~~n~lyn~~t~r-aivvQssf~~~q~R  310 (907)
T KOG2264         256 AELEKLYSLPHWRTDGFNHVLFNLGRPSDTQNLLYNFQTGR-AIVVQSSFYTVQIR  310 (907)
T ss_pred             HHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCEEEECCCC-EEEEEECCEEEEEC
T ss_conf             76666405765567876338997368655666306721572-68985121145312


No 48 
>pfam04799 Fzo_mitofusin fzo-like conserved region. Family of putative transmembrane GTPase. The fzo protein is a mediator of mitochondrial fusion. This conserved region is also found in the human mitofusin protein.
Probab=62.43  E-value=9.7  Score=16.73  Aligned_cols=54  Identities=24%  Similarity=0.307  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH---HHHHHHHHHHHHHCCC
Q ss_conf             89999888799999989999999998875304989999---9999989999984056
Q gi|254780182|r  461 RLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLL---GIIKQELLSVKDELDT  514 (910)
Q Consensus       461 rL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~---~iI~~EL~eik~kygd  514 (910)
                      ||-+...--...++.|.++|.++|..|+.+-+.-+.++   ..+-.||...-+.|=.
T Consensus       113 rLc~qVd~~~~~le~ei~~L~~ei~~LE~iq~~~K~LRnKA~~l~~eL~~F~~~yL~  169 (171)
T pfam04799       113 RLCQQVDVTSKDLEEEIAELTKEIQRLETIQSRSKLLRNKANLLENELEDFTKTFLT  169 (171)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999998689999999999999999999999999899986898999999999997458


No 49 
>PRK03298 hypothetical protein; Provisional
Probab=61.79  E-value=8.4  Score=17.27  Aligned_cols=34  Identities=21%  Similarity=0.170  Sum_probs=18.7

Q ss_pred             ECCCCEEEEEEEC--CCCCEEEEEECCCEEEEEEHH
Q ss_conf             1589857888961--898269999369859997587
Q gi|254780182|r  678 LDSRDEILSVETC--TQENDILLTTKLGQCVRFPIS  711 (910)
Q Consensus       678 LkegD~Li~v~~~--~~~~~Iil~T~~G~~lrF~~~  711 (910)
                      +.+|=+++.--.-  .|--||+..-++|........
T Consensus       119 ie~Gf~~v~rE~~T~~G~VDll~~D~~G~~V~VEiK  154 (224)
T PRK03298        119 LGEGYTLVRREYMTAIGPVDLLCRDADGATVAVEIK  154 (224)
T ss_pred             HCCCCEEEEEEECCCCCCEEEEEECCCCCEEEEEEE
T ss_conf             158989877873179883538998799999999998


No 50 
>KOG0640 consensus
Probab=61.53  E-value=10  Score=16.61  Aligned_cols=24  Identities=17%  Similarity=0.220  Sum_probs=12.8

Q ss_pred             CCCCCCCEEEEECCCCEEEEEEEE
Q ss_conf             515687388980899879999983
Q gi|254780182|r  874 SRATKGVVIFSTAKDERVVSVERI  897 (910)
Q Consensus       874 gR~a~GV~i~~L~~~D~Vv~va~i  897 (910)
                      .|++--+++..|....-+.++.--
T Consensus       382 aRtadr~~l~slgHn~a~R~i~HS  405 (430)
T KOG0640         382 ARTADRVALLSLGHNGAVRWIVHS  405 (430)
T ss_pred             CCCHHHHHHCCCCCCCCCEEEEEC
T ss_conf             654345431025788873489857


No 51 
>PRK10834 hypothetical protein; Provisional
Probab=61.44  E-value=3.6  Score=20.53  Aligned_cols=125  Identities=22%  Similarity=0.251  Sum_probs=61.0

Q ss_pred             HHHHHC--CCCCCCH-HHHH----HHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHH-CCC
Q ss_conf             556643--6688704-7899----999971220111561314788708877697201357-899978999999863-076
Q gi|254780182|r   78 SGEVMG--KYHPHGN-AAIY----DALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERY-TECRLQKAAHFLLDD-LGK  148 (910)
Q Consensus        78 vg~v~g--kyHPHGd-~siy----~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RY-te~rl~~~~~~~l~~-i~~  148 (910)
                      ||-|+|  ||++.|. +..|    ||.+.+=+.=..++.|+.|.  -|+.+.|.|.+||- --.+=- -++.++.| -.-
T Consensus        47 valVLGtak~~~~G~pn~~~~~RldaA~~LY~~GKv~~iLvSGD--n~~~~YnEp~~Mk~~Li~~GV-P~e~I~~D~AGf  123 (239)
T PRK10834         47 VGVVLGTAKYYRTGVINQYYRYRIQGAINAYNSGKVNYLLLSGD--NALQSYNEPMTMRKDLIAAGV-DPADIVLDYAGF  123 (239)
T ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCC--CCCCCCCCHHHHHHHHHHCCC-CHHHEECCCCCC
T ss_conf             69994576467899819899999999999998699748986689--998889828999999998599-899950566765


Q ss_pred             CCCC----CEECCCCCCCCCEECCCCCCC---CHHCCCCCE-EEHHHHCCCC----CCHHHHHHHHHHHHH
Q ss_conf             8405----330689885485034322732---110167610-1013317898----547899999988761
Q gi|254780182|r  149 DTVD----FRPNYDGSFQEPVVLCARYPN---VLVNGGGGI-AVGMATNIPT----HNLGEVVDGCVAVID  207 (910)
Q Consensus       149 ~tv~----~~~n~D~~~~EP~vlP~~~P~---lL~nG~~GI-AvGmaTnipp----HNl~Ev~~a~~~~i~  207 (910)
                      .|-|    -..-|+-  ..-++.--+|-+   |.+--.-|| |+|++..-|-    -.++|+..-+.+++|
T Consensus       124 rT~DS~vRAk~VF~~--~~~iIVTQ~FH~~RAlfiAr~~GidA~g~~a~~~~~~~k~r~RE~~AR~ka~~D  192 (239)
T PRK10834        124 RTLDSIVRTRKVFDT--NDFIIITQRFHCERALFIALHMGIQAQCYAVPSPKNMLSVRVREFAARFGALAD  192 (239)
T ss_pred             CHHHHHHHHHHHHCC--CCEEEEECCHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             489999999998099--828999460138999999997498369971688654411059999999988856


No 52 
>KOG1764 consensus
Probab=60.45  E-value=8.5  Score=17.25  Aligned_cols=17  Identities=18%  Similarity=0.173  Sum_probs=7.2

Q ss_pred             HHHHHHHHHCCCEEEEEE
Q ss_conf             889999870120389999
Q gi|254780182|r  235 TGIKNAYATGRGSIVIRG  252 (910)
Q Consensus       235 ~~i~~~y~tGrG~i~iR~  252 (910)
                      -.+.+|+... +..-+|+
T Consensus        85 ~~v~~a~~~l-~~~~~~~  101 (381)
T KOG1764          85 LSVKKAFNAL-VQNGVRA  101 (381)
T ss_pred             CCHHHHHHHH-HHHEEEE
T ss_conf             8499999988-8623763


No 53 
>COG3953 SLT domain proteins [General function prediction only]
Probab=60.29  E-value=3.6  Score=20.54  Aligned_cols=23  Identities=43%  Similarity=0.670  Sum_probs=16.7

Q ss_pred             CCCCCCC-CCCCCCCHHHHHHHHHH
Q ss_conf             7887088-77697201357899978
Q gi|254780182|r  113 GQGNFGS-VDGDPPAAERYTECRLQ  136 (910)
Q Consensus       113 g~GnfGs-~dgd~~AA~RYte~rl~  136 (910)
                      |||||=. +| -.+|||||++.|+-
T Consensus        66 g~~ni~Npid-na~AAi~yi~~rYG   89 (235)
T COG3953          66 GQGNILNPID-NAAAAIRYIKTRYG   89 (235)
T ss_pred             CCCCHHCHHH-HHHHHHHHHHHHCC
T ss_conf             7400003266-89999998862225


No 54 
>KOG0243 consensus
Probab=60.07  E-value=11  Score=16.41  Aligned_cols=25  Identities=28%  Similarity=0.363  Sum_probs=12.6

Q ss_pred             CCCCCEEEHHHHCCCCCCHHHHHHH
Q ss_conf             1676101013317898547899999
Q gi|254780182|r  177 NGGGGIAVGMATNIPTHNLGEVVDG  201 (910)
Q Consensus       177 nG~~GIAvGmaTnippHNl~Ev~~a  201 (910)
                      +|-.|+-|-=.--||-||-.|+..-
T Consensus       220 ~~kggV~vkGlEEi~V~~A~ei~kl  244 (1041)
T KOG0243         220 DGKGGVIVKGLEEIIVTNADEIYKL  244 (1041)
T ss_pred             CCCCCEEEECCEEEEECCHHHHHHH
T ss_conf             7868679743526653465689999


No 55 
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=60.00  E-value=11  Score=16.40  Aligned_cols=63  Identities=17%  Similarity=0.223  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             999987899998887999999899999999988753049899999999989999984056883
Q gi|254780182|r  455 RAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRR  517 (910)
Q Consensus       455 ~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RR  517 (910)
                      .++=+++=++==.-|...++.....|..++.++.+.+..-+.........+..+.+.+++.|.
T Consensus        83 ~~v~~~~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~~~e~~~~e~~~  145 (239)
T COG1579          83 SAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLEKNLAEAEA  145 (239)
T ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             612569999987889999999999999999999999998898899889999999988999999


No 56 
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=59.67  E-value=11  Score=16.36  Aligned_cols=25  Identities=20%  Similarity=0.259  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      |+||++|-+||++....+|-.+.-+
T Consensus        43 ~~Lt~eqk~aV~~RD~~~ll~~Ggn   67 (106)
T cd07925          43 FGLTPEQKQAVRNRDVLRMLEAGGN   67 (106)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             6999999999997369999990663


No 57 
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family; InterPro: IPR014243    This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria). In some species these proteins are encoded multiple times. The best characterised protein in this entry is the prespore-specific transcription factor RsfA from Bacillus subtilis, previously known as YwfN. Expression of RsfA is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. A paralog in B. subtilis is designated YlbO, though its function is not known. A highly variable linker region separates two very strongly conserved sequence regions within the protein. .
Probab=59.55  E-value=11  Score=16.34  Aligned_cols=105  Identities=17%  Similarity=0.218  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             999999999999988-8778999999874069999998618997898787763126978899999740221112223445
Q gi|254780182|r  368 VVVRRTKYLLNKARD-RAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGT  446 (910)
Q Consensus       368 vi~rRt~~~L~ka~~-R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  446 (910)
                      +|+++++-.++.|++ |.|---.--..-.-|..||....+-++...+-..                              
T Consensus        54 ~VRk~Y~~aI~lAKK~RK~~KRak~~~~lTl~~VI~FLq~~~~~~~~~~~------------------------------  103 (163)
T TIGR02894        54 VVRKRYEEAIELAKKQRKERKRAKKAESLTLQDVISFLQNLKTTNPSDQA------------------------------  103 (163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH------------------------------
T ss_conf             87585899999998861478864378626878899999998887799999------------------------------


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf             236999999999878999988879999998999999999887530498999999999899999840568833100
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIV  521 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~  521 (910)
                                         ...|.++|.+|...|.+++++|++=|..=.....+|-++-..+.+--.-.|+=.+.
T Consensus       104 -------------------l~~E~~~L~~~~~~Lq~~ne~L~~el~~L~~~~~~~eEDY~~L~~IMdRARkl~~~  159 (163)
T TIGR02894       104 -------------------LQKENERLKKELESLQKRNEELEKELEKLEKRQSTIEEDYETLIDIMDRARKLAVV  159 (163)
T ss_pred             -------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             -------------------99899999999999999999999999999998467899999999999887375440


No 58 
>pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown.
Probab=58.87  E-value=10  Score=16.56  Aligned_cols=32  Identities=19%  Similarity=0.060  Sum_probs=15.6

Q ss_pred             ECCCCEEEEEEECC--CCCEEEEEECCCEEEEEE
Q ss_conf             15898578889618--982699993698599975
Q gi|254780182|r  678 LDSRDEILSVETCT--QENDILLTTKLGQCVRFP  709 (910)
Q Consensus       678 LkegD~Li~v~~~~--~~~~Iil~T~~G~~lrF~  709 (910)
                      +.+|=+++.--.-.  |--||+..-++|......
T Consensus       120 ie~G~~~v~rE~~T~~G~VDil~~D~~G~~VvVE  153 (228)
T pfam01939       120 IEEGFKPVRREYQIAHGIVDILGKDEDGNIVILE  153 (228)
T ss_pred             HCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEE
T ss_conf             2489899988852588736689987999999999


No 59 
>PHA00728 hypothetical protein
Probab=58.64  E-value=11  Score=16.22  Aligned_cols=66  Identities=14%  Similarity=0.181  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             8879999998999999999887530498999999999899999840568833100134345301014567818999079
Q gi|254780182|r  467 GLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSHL  545 (910)
Q Consensus       467 ~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~  545 (910)
                      +.|.+.|+.|-++|.++.++|+.+++++..-.   -+++.+|-+-|-..-|+          +.+|+...+.+..||.+
T Consensus         4 ~teveql~keneelkkkla~leal~nne~~~~---~e~~~eiEnPYTVTNRa----------IsElV~PkDTMfYLsgn   69 (153)
T PHA00728          4 KTEVEQLKKENEELKKKLAKLEALLNNESAEE---EEELQEIENPYTVTNRA----------ITELVEPKDTMFYLSGN   69 (153)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH---HHHHHHHCCCCEEHHHH----------HHHHCCCCCCEEEECCC
T ss_conf             46899999866999999999999974788503---56687723871220578----------88755976415886377


No 60 
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=58.34  E-value=11  Score=16.18  Aligned_cols=25  Identities=28%  Similarity=0.270  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      |+||++|-+||++....+|-.+.-+
T Consensus        54 ~~Lteeqr~aV~~RD~~~ll~lGgn   78 (117)
T PRK13378         54 YGLNEEQKEAIRNRDVLQLLAAGGN   78 (117)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             6999999999997379999994674


No 61 
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=58.07  E-value=8  Score=17.47  Aligned_cols=47  Identities=34%  Similarity=0.615  Sum_probs=36.4

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHCC--CCCHH--HHHHHHCCCCCEEEE
Q ss_conf             5999924644352899999999998716--65014--458730374655799
Q gi|254780182|r  264 EQIVVTEIPYQVNKAAMLEKIAELVREK--RIVDI--ADLRDESDRQGYRVV  311 (910)
Q Consensus       264 ~~ivItEiPY~vnk~~lie~Ia~lv~~~--ki~gI--~dirDeSdr~giRiv  311 (910)
                      -+|.||--| +|.|+.++.+|++..+++  ++-|+  ..||+.--|.|.+||
T Consensus         6 mki~ITG~P-GvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR~gGkR~GF~Iv   56 (179)
T COG1618           6 MKIFITGRP-GVGKTTLVLKIAEKLREKGYKVGGFITPEVREGGKRIGFKIV   56 (179)
T ss_pred             EEEEEECCC-CCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCEEEEEEEE
T ss_conf             599986799-845899999999999855966513983114208827515999


No 62 
>pfam07914 DUF1679 Protein of unknown function (DUF1679). The region featured in this family is found in a number of C. elegans proteins, in one case as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in ZnF_C4 and HLH domain-containing kinases. In fact, one member of this family is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins (Interpro:IPR000536, Interpro:IPR008946, and Interpro:IPR001628).
Probab=57.93  E-value=5.4  Score=18.97  Aligned_cols=64  Identities=19%  Similarity=0.243  Sum_probs=46.8

Q ss_pred             EEEHHHHCCCCCCHHHHHHHHHHHHHC-CCCCHHHHHHHCCCCCCCC--CCCCCCHHHHHHHHHHCCC
Q ss_conf             010133178985478999999887618-7768888886345866887--4434475889999870120
Q gi|254780182|r  182 IAVGMATNIPTHNLGEVVDGCVAVIDN-PDIDLDALMEIIRGPDFPT--GAVILGRTGIKNAYATGRG  246 (910)
Q Consensus       182 IAvGmaTnippHNl~Ev~~a~~~~i~~-p~~~~~eL~~~i~GPDFPT--GG~I~~~~~i~~~y~tGrG  246 (910)
                      ..++|-.|+||..|-.|++|+..+-.. -..+.+|. +.+.||||.-  =+..++.+++...|..=|.
T Consensus       161 ~~~~~y~ni~~deL~~vv~~iA~fqA~~~~LseEE~-k~i~g~df~~~~~~~~~~~~~~~~~f~~lr~  227 (413)
T pfam07914       161 HTRHMYENIPADELIPVLRAIATFQALGESLSEEEK-KSANGADFLEQMFETFMSEEGLKGIFDQLRN  227 (413)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             687254898989999999999999986434998997-5356757999999987236779999999975


No 63 
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=57.76  E-value=11  Score=16.11  Aligned_cols=80  Identities=24%  Similarity=0.296  Sum_probs=40.2

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998618997898787763126978899999740221112223445236999999999878999988879999998999
Q gi|254780182|r  400 VVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNS  479 (910)
Q Consensus       400 VI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~e  479 (910)
                      .++.||+  +++.-+++|.++                           +-+....+.|++|--      ++.++..+.++
T Consensus         3 d~k~ir~--n~d~v~~~l~~r---------------------------~~~~~~~~~~~~ld~------~~r~~~~~~e~   47 (429)
T COG0172           3 DLKLIRE--NPDAVREKLKKR---------------------------GGDALDVDKLLELDE------ERRKLLRELEE   47 (429)
T ss_pred             HHHHHHH--CHHHHHHHHHHC---------------------------CCCHHHHHHHHHHHH------HHHHHHHHHHH
T ss_conf             4877650--999999987634---------------------------883767899999999------99999999999


Q ss_pred             HHHHHHHHHHHHCC----HHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99999988753049----899999999989999984056
Q gi|254780182|r  480 LGIEIKECLDILSS----RSRLLGIIKQELLSVKDELDT  514 (910)
Q Consensus       480 L~~~I~~l~~IL~s----~~~l~~iI~~EL~eik~kygd  514 (910)
                      |+.+.+.+.+.++.    ...-..-++.|..+++++..+
T Consensus        48 l~~~rn~~sk~ig~~~~~~~~~~~~l~~e~~~l~~~l~~   86 (429)
T COG0172          48 LQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKE   86 (429)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             999988999999987632621489999988988899872


No 64 
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. 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.
Probab=57.72  E-value=11  Score=16.10  Aligned_cols=25  Identities=36%  Similarity=0.472  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      |+||++|-+||++....+|-.+.-+
T Consensus        43 ~~Lt~eqk~aV~~RD~~~ll~~Ggn   67 (106)
T cd07921          43 FGLTEEQKQAVLDRDWLRLLELGGN   67 (106)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             6999999999997369999990663


No 65 
>KOG3985 consensus
Probab=57.70  E-value=11  Score=16.10  Aligned_cols=84  Identities=29%  Similarity=0.414  Sum_probs=47.5

Q ss_pred             CCCCCC---CE--ECCCCC-------CCCHHCCCCCEEEH--HHHCCCCCC--HHHHHHHHHHHHHCCCCCHHHHHHHCC
Q ss_conf             988548---50--343227-------32110167610101--331789854--789999998876187768888886345
Q gi|254780182|r  158 DGSFQE---PV--VLCARY-------PNVLVNGGGGIAVG--MATNIPTHN--LGEVVDGCVAVIDNPDIDLDALMEIIR  221 (910)
Q Consensus       158 D~~~~E---P~--vlP~~~-------P~lL~nG~~GIAvG--maTnippHN--l~Ev~~a~~~~i~~p~~~~~eL~~~i~  221 (910)
                      =||++|   |.  |||-.|       |+-.-+|+---|-|  --.--||++  ++|++-.+-.-+.+|.-+ +--+-.|.
T Consensus        95 cGSLre~I~Pgd~v~p~q~IDrTt~R~~tffdg~~~~a~gVcHv~~~~pf~~k~reil~~~a~~l~~~~hd-~~tvVciE  173 (283)
T KOG3985          95 CGSLREEIKPGDFVLPDQIIDRTTGRPSTFFDGSYDQAGGVCHVPFGPPFSQKLREILISTAKELTNPHHD-DGTVVCIE  173 (283)
T ss_pred             CCCCCCCCCCCCEECCHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCCCCCC-CEEEEEEE
T ss_conf             24443458986675634554443367531115754578826761678872789999999998872687678-53699851


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCEEE
Q ss_conf             8668874434475889999870120389
Q gi|254780182|r  222 GPDFPTGAVILGRTGIKNAYATGRGSIV  249 (910)
Q Consensus       222 GPDFPTGG~I~~~~~i~~~y~tGrG~i~  249 (910)
                      ||-|.|-+.       -..|++--|++.
T Consensus       174 GPrFStRAE-------S~mfR~wGa~vI  194 (283)
T KOG3985         174 GPRFSTRAE-------SKMFRSWGASVI  194 (283)
T ss_pred             CCCCCHHHH-------HHHHHHHCCCEE
T ss_conf             786541788-------889987451533


No 66 
>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.     This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place.    More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=57.61  E-value=3.1  Score=21.11  Aligned_cols=22  Identities=14%  Similarity=0.163  Sum_probs=10.1

Q ss_pred             CHHHHHHHHHHHHHH-HHHHCCC
Q ss_conf             989999999998999-9984056
Q gi|254780182|r  493 SRSRLLGIIKQELLS-VKDELDT  514 (910)
Q Consensus       493 s~~~l~~iI~~EL~e-ik~kygd  514 (910)
                      |--++-+--++|.+. |.+.||+
T Consensus       347 DS~~lS~~A~~eaR~~I~~~yG~  369 (688)
T TIGR01051       347 DSTRLSNEAVNEARNLIDKNYGK  369 (688)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCH
T ss_conf             30578999999999888862112


No 67 
>KOG0291 consensus
Probab=57.24  E-value=12  Score=16.04  Aligned_cols=152  Identities=19%  Similarity=0.231  Sum_probs=73.5

Q ss_pred             CCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCC--EEEEEECCCCEEEEECCCCCCC
Q ss_conf             14567818999079705233100000233456521100014641010113323777--3999954893999820004322
Q gi|254780182|r  532 CIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHT--SVLFFSSLGFVYKEKVWRLPIG  609 (910)
Q Consensus       532 lI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d--~LLfFTs~Gkvy~l~v~~IP~~  609 (910)
                      +-..-.+++..|-+|-++...+.-||--+       ..   ..... ..|.|-+-|  -.+.+--.=-+|-+.+|.+..|
T Consensus       400 f~~~g~~llssSLDGtVRAwDlkRYrNfR-------Tf---t~P~p-~QfscvavD~sGelV~AG~~d~F~IfvWS~qTG  468 (893)
T KOG0291         400 FTARGNVLLSSSLDGTVRAWDLKRYRNFR-------TF---TSPEP-IQFSCVAVDPSGELVCAGAQDSFEIFVWSVQTG  468 (893)
T ss_pred             EEECCCEEEEEECCCEEEEEEECCCCEEE-------EE---CCCCC-EEEEEEEECCCCCEEEEECCCEEEEEEEEEECC
T ss_conf             99628789996238717843410332024-------31---27886-036688875888789960466178999980057


Q ss_pred             CCCCCCCCCEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCC-EEEEEECCCCEEEEE
Q ss_conf             44456554124545-3655620025663012566687179999479918984236862047772-278661589857888
Q gi|254780182|r  610 SPQARGKALINILS-LNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSG-KIAMKLDSRDEILSV  687 (910)
Q Consensus       610 sr~skG~pi~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G-~~aikLkegD~Li~v  687 (910)
                                ++++ |...|--+.-++++.     ....|.-.+=+-.|+....  |.   ++| .--+.+.  -.+..+
T Consensus       469 ----------qllDiLsGHEgPVs~l~f~~-----~~~~LaS~SWDkTVRiW~i--f~---s~~~vEtl~i~--sdvl~v  526 (893)
T KOG0291         469 ----------QLLDILSGHEGPVSGLSFSP-----DGSLLASGSWDKTVRIWDI--FS---SSGTVETLEIR--SDVLAV  526 (893)
T ss_pred             ----------EEEEHHCCCCCCCEEEEECC-----CCCEEEECCCCCEEEEEEE--EC---CCCEEEEEEEC--CCEEEE
T ss_conf             ----------14301327777610257756-----6686775135542788886--32---67603567602--211378


Q ss_pred             EECCCCCEEEEEECCCEEEEEEHHHCCCC
Q ss_conf             96189826999936985999758762354
Q gi|254780182|r  688 ETCTQENDILLTTKLGQCVRFPISAIRVF  716 (910)
Q Consensus       688 ~~~~~~~~Iil~T~~G~~lrF~~~evr~~  716 (910)
                      ..-..+.+++++|-+|.+-.|+..+--.+
T Consensus       527 sfrPdG~elaVaTldgqItf~d~~~~~q~  555 (893)
T KOG0291         527 SFRPDGKELAVATLDGQITFFDIKEAVQV  555 (893)
T ss_pred             EECCCCCEEEEEEECCEEEEEEHHHCEEE
T ss_conf             87479976889981564899882354241


No 68 
>PRK04247 hypothetical protein; Provisional
Probab=57.01  E-value=11  Score=16.40  Aligned_cols=35  Identities=23%  Similarity=0.127  Sum_probs=20.3

Q ss_pred             ECCCCEEEEEEECC--CCCEEEEEECCCEEEEEEHHH
Q ss_conf             15898578889618--982699993698599975876
Q gi|254780182|r  678 LDSRDEILSVETCT--QENDILLTTKLGQCVRFPISA  712 (910)
Q Consensus       678 LkegD~Li~v~~~~--~~~~Iil~T~~G~~lrF~~~e  712 (910)
                      +.+|=+++.--.-.  |--||+..-+.|........-
T Consensus       144 ie~G~~~v~rE~~T~~G~VDil~~D~~G~~V~VEvKR  180 (250)
T PRK04247        144 IEEGFRPVAREYETPAGIIDILGRDKEGNLVVLELKR  180 (250)
T ss_pred             HCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEE
T ss_conf             2589889988873598846489987998999999971


No 69 
>pfam01401 Peptidase_M2 Angiotensin-converting enzyme. Members of this family are dipeptidyl carboxydipeptidases (cleave carboxyl dipeptides) and most notably convert angiotensin I to angiotensin II. Many members of this family contain a tandem duplication of the 600 amino acid peptidase domain, both of these are catalytically active. Most members are secreted membrane bound ectoenzymes.
Probab=56.55  E-value=9.7  Score=16.70  Aligned_cols=40  Identities=10%  Similarity=0.122  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             8879999998999999999887530498999999999899999840568
Q gi|254780182|r  467 GLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       467 ~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      ..|-..++++.+.|-.+++=|=+-      |-..+..+   +.++||++
T Consensus       195 ~Ye~~~f~~~~e~lw~qvkPLY~~------LHayVR~k---L~~~YG~~  234 (595)
T pfam01401       195 WYESPTLEQDLERLYQELQPLYLN------LHAYVRRA---LHRHYGDQ  234 (595)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHH---HHHHCCCC
T ss_conf             631143999999999998899999------99999999---99866621


No 70 
>KOG1507 consensus
Probab=56.44  E-value=7.8  Score=17.57  Aligned_cols=74  Identities=18%  Similarity=0.244  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC------CCCEEECCCCC
Q ss_conf             999999878999988879999998999999999887530498999999999899999840568------83310013434
Q gi|254780182|r  453 QTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTP------RRTRIVEGLLD  526 (910)
Q Consensus       453 QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~------RRT~I~~~~~~  526 (910)
                      +.-+-+.+||..|..+...-+++=-...+++|..|+.|-..-..+-.-..+|.-+|-.||...      ||.+|+....+
T Consensus        48 ~~~~~~~~r~~~l~~~~s~~v~~Lp~~Vk~Rv~aLk~lQ~~~~~ie~~F~~e~~~LE~ky~~~yqplfdkR~eIi~g~~E  127 (358)
T KOG1507          48 KLLSALDGRLASLAGLLSDMVENLPPAVKNRVLALKNLQLECDEIEAKFQEEVHELERKYAKLYQPLFDKRREIINGEVE  127 (358)
T ss_pred             HHHCCCCHHHHCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCC
T ss_conf             55413411331346778046665699999999999998999999999999999999999998756499999999707766


No 71 
>pfam08082 PRO8NT PRO8NT (NUC069), PrP8 N-terminal domain. The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region.
Probab=55.44  E-value=10  Score=16.50  Aligned_cols=56  Identities=30%  Similarity=0.543  Sum_probs=39.6

Q ss_pred             CCHHH-HHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH-HCCCCCC
Q ss_conf             97367-899999998789999981134042556643668870478999999712201-1156131
Q gi|254780182|r   49 LKPVH-RRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQDW-SLRLLLI  111 (910)
Q Consensus        49 lKpv~-Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~-~~r~pli  111 (910)
                      +-|-| |+|+   .+-|-.+++.|+.--|+.=.-| ||-||   |||--|-+|-|+| ..||.=|
T Consensus         4 mPPEhlRKIi---~dhgDmsskkf~~dkr~~lgaL-kY~Ph---Av~KLLEnmPmPWE~~r~V~V   61 (152)
T pfam08082         4 MPPEHLRKII---KDHGDMSSKKFASDKRSYLGAL-KYMPH---ALLKLLENMPMPWEQVRYVKV   61 (152)
T ss_pred             CCHHHHHHHH---HHCCCCCHHHCCHHHHHHHHHH-HHHHH---HHHHHHHCCCCCHHHHCCEEE
T ss_conf             9879999999---7445744011011358887677-54268---999998718985777403247


No 72 
>KOG0315 consensus
Probab=55.18  E-value=12  Score=15.78  Aligned_cols=107  Identities=8%  Similarity=0.136  Sum_probs=57.7

Q ss_pred             CEEEEEECCCCEE------EEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEE
Q ss_conf             7399995489399------9820004322444565541245453655620025663012566687179999479918984
Q gi|254780182|r  587 TSVLFFSSLGFVY------KEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRN  660 (910)
Q Consensus       587 d~LLfFTs~Gkvy------~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt  660 (910)
                      =.-|-+|+.++..      .++.|+|-.++    -.|+.+|-.-..+  |+ .+.|.     .+...+.-.+.+|.+|--
T Consensus        43 VNrLeiTpdk~~LAaa~~qhvRlyD~~S~n----p~Pv~t~e~h~kN--Vt-aVgF~-----~dgrWMyTgseDgt~kIW  110 (311)
T KOG0315          43 VNRLEITPDKKDLAAAGNQHVRLYDLNSNN----PNPVATFEGHTKN--VT-AVGFQ-----CDGRWMYTGSEDGTVKIW  110 (311)
T ss_pred             EEEEEECCCCCHHHHCCCCEEEEEECCCCC----CCCEEEEECCCCC--EE-EEEEE-----ECCEEEEECCCCCEEEEE
T ss_conf             206997687124543248706999746899----9953687636786--68-99972-----357698854888348998


Q ss_pred             CHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHH
Q ss_conf             2368620477722786615898578889618982699993698599975876
Q gi|254780182|r  661 KLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISA  712 (910)
Q Consensus       661 ~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~e  712 (910)
                      .+....-.|-       ++-.--+-.+.+-....+++..+.+|.+=..+..+
T Consensus       111 dlR~~~~qR~-------~~~~spVn~vvlhpnQteLis~dqsg~irvWDl~~  155 (311)
T KOG0315         111 DLRSLSCQRN-------YQHNSPVNTVVLHPNQTELISGDQSGNIRVWDLGE  155 (311)
T ss_pred             ECCCCCCCCC-------CCCCCCCCEEEECCCCCEEEEECCCCCEEEEECCC
T ss_conf             6247021100-------15789743587469861488605878789987167


No 73 
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241    This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. .
Probab=53.61  E-value=7.1  Score=17.95  Aligned_cols=12  Identities=25%  Similarity=0.816  Sum_probs=4.5

Q ss_pred             HHHHHHHHHCCC
Q ss_conf             899999998789
Q gi|254780182|r   54 RRILFGMMQMGV   65 (910)
Q Consensus        54 Rrily~m~~~~~   65 (910)
                      ||+||++|+.||
T Consensus        48 Rk~Ly~LYdagl   59 (168)
T TIGR00373        48 RKLLYKLYDAGL   59 (168)
T ss_pred             HHHHHHHHCCEE
T ss_conf             899998730301


No 74 
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=53.42  E-value=13  Score=15.56  Aligned_cols=25  Identities=20%  Similarity=0.171  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      |+||++|-+||++-....|..+.-+
T Consensus        55 ~~LTeEqk~aV~~RDw~~li~~Ggn   79 (119)
T PRK13379         55 ADLTEQEKELIRARDWLGLVQYGAN   79 (119)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             5999999999996159999984763


No 75 
>PRK07773 replicative DNA helicase; Validated
Probab=52.63  E-value=13  Score=15.47  Aligned_cols=41  Identities=15%  Similarity=0.261  Sum_probs=20.2

Q ss_pred             CEEEEEECCCEEEEEECCCC--CCC-CCCCCCCEEEEECCC--CEEEEE
Q ss_conf             64999945998999990105--544-515687388980899--879999
Q gi|254780182|r  851 DQIILVSDKGTLIRVPVNEI--RIA-SRATKGVVIFSTAKD--ERVVSV  894 (910)
Q Consensus       851 DeIlliT~~G~iiR~~v~~I--~~~-gR~a~GV~i~~L~~~--D~Vv~v  894 (910)
                      |+|.-|+.-|.-   .|.++  |-+ .=.|+|..+-|--+-  |-|+.+
T Consensus       776 DeIvsIe~~Gee---eVyDLTVpgtHNFVAndIivHNSIEQDAD~vi~l  821 (868)
T PRK07773        776 DEIVEITSIGEE---EVFDGTVPGTHNFVANGISVHNSIEQDADLVILL  821 (868)
T ss_pred             EEEEEEEECCCE---EEEEEECCCCCCCEECCEEECCCCCCCCCEEEEE
T ss_conf             458999887850---2577635676530056752116613247789997


No 76 
>pfam06572 DUF1131 Protein of unknown function (DUF1131). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=52.35  E-value=14  Score=15.43  Aligned_cols=31  Identities=39%  Similarity=0.601  Sum_probs=17.9

Q ss_pred             CCEEEEEECCCCCEEEEE-E--CCCEEEEEECCC
Q ss_conf             868999972899649999-4--599899999010
Q gi|254780182|r  839 GALVAVFPVNDNDQIILV-S--DKGTLIRVPVNE  869 (910)
Q Consensus       839 g~lv~~~~V~~~DeIlli-T--~~G~iiR~~v~~  869 (910)
                      |.+|..+..-.+|++-|+ +  .+|++-|+.|.+
T Consensus        79 G~iv~~fqAmk~d~V~lvI~G~~kGtV~RI~V~D  112 (192)
T pfam06572        79 GQIVRYFQAMKGDQVKLVINGQPKGTVSRIDVMD  112 (192)
T ss_pred             CEEEEEEEEECCCCEEEEEECCCCCEEEEEEEEC
T ss_conf             8199998760688179999668886499999855


No 77 
>pfam01208 URO-D Uroporphyrinogen decarboxylase (URO-D).
Probab=52.32  E-value=14  Score=15.43  Aligned_cols=29  Identities=7%  Similarity=-0.042  Sum_probs=17.7

Q ss_pred             HHHCCHHCCCCCEEEEEECCCCCCCCHHH
Q ss_conf             97610110000002455416630002999
Q gi|254780182|r  328 YRYTSLQSLFSVNMVALNGYKPERFTLIG  356 (910)
Q Consensus       328 yk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~  356 (910)
                      -.+...|..-++..+.+.|.-.-.|+-..
T Consensus       182 ~~~~~~qi~aGad~i~i~Ds~~~~ls~~~  210 (337)
T pfam01208       182 IEYLKAQIEAGADAIQIFDSWAGLLSPED  210 (337)
T ss_pred             HHHHHHHHHHCCCEEEEECCCCCCCCHHH
T ss_conf             99999999829967998347888789899


No 78 
>pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.).
Probab=51.04  E-value=12  Score=15.85  Aligned_cols=33  Identities=27%  Similarity=0.541  Sum_probs=21.8

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHC
Q ss_conf             97367899999998789999981134042556643
Q gi|254780182|r   49 LKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMG   83 (910)
Q Consensus        49 lKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~g   83 (910)
                      |-|+||.||.+.-++-...+.| .||..|. +.++
T Consensus         2 LT~~Qr~IL~aLI~lY~~~~~p-Vks~~IA-e~l~   34 (79)
T pfam03444         2 LTPVQKEILQALINLYRKKGRA-VKGEEIA-DIIG   34 (79)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCC-CCHHHHH-HHHC
T ss_conf             7789999999999999972998-6679999-9987


No 79 
>TIGR02687 TIGR02687 conserved hypothetical protein TIGR02687; InterPro: IPR014060   Members of this family are uncharacterised proteins sporadically distributed in bacteria and archaea, about 880 amino acids in length. Proteins in this entry are encoded by genes that are repeatedly found upstream of another uncharacterised gene which encodes proteins of about 470 amino acids in length (see IPR014061 from INTERPRO)..
Probab=50.49  E-value=14  Score=15.22  Aligned_cols=11  Identities=27%  Similarity=0.555  Sum_probs=5.6

Q ss_pred             EEEEC-CCCEEE
Q ss_conf             99947-991898
Q gi|254780182|r  649 VFATK-HGNVRR  659 (910)
Q Consensus       649 vl~Tk-~G~VKk  659 (910)
                      |+||. +|++-+
T Consensus       676 ilVTADHGFlYq  687 (911)
T TIGR02687       676 ILVTADHGFLYQ  687 (911)
T ss_pred             EEEECCCCHHHH
T ss_conf             588415561445


No 80 
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=50.40  E-value=14  Score=15.20  Aligned_cols=51  Identities=16%  Similarity=0.034  Sum_probs=39.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHCCHHHH
Q ss_conf             23699999999987899998887999999899999--9999887530498999
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRDDIRNELNSLG--IEIKECLDILSSRSRL  497 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~--~~I~~l~~IL~s~~~l  497 (910)
                      -+||-.|+.+.+.+|++-|..||..++..=-.+.-  --|+.|-+.|+-+...
T Consensus        15 ~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~   67 (284)
T COG1426          15 KGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDE   67 (284)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHH
T ss_conf             49999999988577599999986677010641576789999999996899899


No 81 
>TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006219   Members of this group catalyze the first enzymatic reaction of the shikimate pathway. The common (shikimate) pathway links metabolism of carbohydrates to biosynthesis of aromatic amino acids phenylalanine, tyrosine, tryptophan, and derivatives in microorganisms and in plants. In a sequence of seven enzymatic reactions, D-erythrose 4-phosphate (E4P), an intermediate of the pentose phosphate pathway, and phosphoenol pyruvate (PEP), a glycolytic intermediate, are converted to chorismate. The pathway begins with the stereospecific condensation of E4P and PEP to yield 7-phospho 2-dehydro 3-deoxy-D-arabino-heptulosonate (DAHP), catalyzed by 3-deoxy-7-phosphoheptulonate synthase (DAHPS) (EC 2.5.1.54, formerly EC 4.1.2.15). The divalent metal cation requirement of this enzyme can be satisfied by a broad range of metals . A Cys residue in a Cys-X-X-His motif has been identified as part of a metal binding site . In Escherichia coli, the enzyme exists in three isoforms, each specifically inhibited by one of the three aromatic amino acids.   DAHP synthetases fall into two classes, class I (represented by this entry) and class II (represented by PIRSF015573 from PIRSF). Class I was believed to be limited to microorganisms and class II to plants. However, a more recent study showed that class II also contains enzymes from a microbial eukaryote and several bacteria . Brick and Woodard  proposed that the difference between the two classes lies in their metal ion requirement for activity. Whereas class I requires no metal cation, class II is dependent on a metal cation for activity. However, recently a class I DAHP synthase from Thermotoga maritima has been purified, characterised, and shown to be a metalloenzyme .   The three-dimentional structures of DAHP synthases have been determined , , , , . The DAHPS(Phe) monomer is a (beta/alpha)8 barrel with an additional N-terminal beta strand and helices and an extra beta sheet near the C terminus . The active site is located in a cleft at the carboxyl end of the barrel . The allosteric feedback inhibition binding site of DAHPS(Phe) is composed of residues from two adjacent subunits of a tight dimer and is at least 20 angstroms away from the closest active site .   The absence of the shikimate pathway in animals makes it an attractive target for nontoxic herbicidal, antimicrobial, and antifungal agents. The nontoxic herbicide glyphosphate competitively inhibits 3-phosphoshikimate 1-carboxyvinyltransferase, the sixth enzymatic reaction of the pathway.; GO: 0003849 3-deoxy-7-phosphoheptulonate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=50.39  E-value=11  Score=16.28  Aligned_cols=30  Identities=7%  Similarity=0.150  Sum_probs=14.5

Q ss_pred             EEEEECCCCCEEEEEECCCEE-EEEEHHHCC
Q ss_conf             888961898269999369859-997587623
Q gi|254780182|r  685 LSVETCTQENDILLTTKLGQC-VRFPISAIR  714 (910)
Q Consensus       685 i~v~~~~~~~~Iil~T~~G~~-lrF~~~evr  714 (910)
                      ..+.-|.|+.+-.++=+.|+. =-|+..+|.
T Consensus       217 ~ai~~T~GN~~~HiILRGG~~GPNY~a~~V~  247 (348)
T TIGR00034       217 MAIVQTSGNPDGHIILRGGKKGPNYDAADVA  247 (348)
T ss_pred             EEEEECCCCCCCEEEECCCCCCCCCCHHHHH
T ss_conf             6787526798524886168767688988899


No 82 
>KOG1359 consensus
Probab=50.30  E-value=12  Score=15.86  Aligned_cols=12  Identities=25%  Similarity=0.482  Sum_probs=4.5

Q ss_pred             CCCCCHHCCCCC
Q ss_conf             273211016761
Q gi|254780182|r  170 RYPNVLVNGGGG  181 (910)
Q Consensus       170 ~~P~lL~nG~~G  181 (910)
                      +.|.+-+.|+++
T Consensus        56 q~p~i~v~G~~k   67 (417)
T KOG1359          56 QGPTIQVKGSDK   67 (417)
T ss_pred             CCCEEEEECCCC
T ss_conf             564499812665


No 83 
>pfam07746 LigA Aromatic-ring-opening dioxygenase LigAB, LigA subunit. This is a family of aromatic ring opening dioxygenases which catalyse the ring-opening reaction of protocatechuate and related compounds.
Probab=49.64  E-value=15  Score=15.11  Aligned_cols=25  Identities=28%  Similarity=0.264  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      |+||+.|-+||++-...+|..+.-+
T Consensus        28 ~~Lt~eqr~av~~rD~~~L~~~G~n   52 (88)
T pfam07746        28 YGLTEEQKAAVRARDWNGLIALGGN   52 (88)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             7999999999982669999994585


No 84 
>PRK06904 replicative DNA helicase; Validated
Probab=49.60  E-value=15  Score=15.10  Aligned_cols=23  Identities=26%  Similarity=0.423  Sum_probs=14.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98999999999899999840568
Q gi|254780182|r  493 SRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       493 s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      ++......|-..|+.+.+.++-|
T Consensus       354 ~r~~ei~~isr~LK~lAkel~ip  376 (472)
T PRK06904        354 NRTLEIAEISRSLKALAKELKVP  376 (472)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             78899999999999999997998


No 85 
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=49.28  E-value=15  Score=15.06  Aligned_cols=25  Identities=16%  Similarity=0.033  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      |+||++|-+||++....+|..+.-+
T Consensus        35 ~~Lt~eqk~av~~RDw~~mi~~Ggn   59 (94)
T cd07923          35 AGLTEEERTLIRNRDWIGMIRYGVI   59 (94)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             6999999999996169999983764


No 86 
>KOG3584 consensus
Probab=49.26  E-value=15  Score=15.06  Aligned_cols=19  Identities=16%  Similarity=0.083  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHCCC
Q ss_conf             9999999989999984056
Q gi|254780182|r  496 RLLGIIKQELLSVKDELDT  514 (910)
Q Consensus       496 ~l~~iI~~EL~eik~kygd  514 (910)
                      .+++-+++||+.+|+.|-.
T Consensus       326 NQNKaLIEELKtLKeLYc~  344 (348)
T KOG3584         326 NQNKALIEELKTLKELYCH  344 (348)
T ss_pred             CCCHHHHHHHHHHHHHHHC
T ss_conf             1458999999989998623


No 87 
>PRK10718 hypothetical protein; Provisional
Probab=49.05  E-value=15  Score=15.04  Aligned_cols=59  Identities=36%  Similarity=0.602  Sum_probs=31.6

Q ss_pred             EEEEECCCCEEEEEHHH-------------CCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEE--ECCCEEEE
Q ss_conf             99997599345301788-------------4866757741488760677776868999972899649999--45998999
Q gi|254780182|r  800 ILTVSEKGFGKRTSSYD-------------FRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILV--SDKGTLIR  864 (910)
Q Consensus       800 IL~vTe~G~GKRt~~~e-------------yr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlli--T~~G~iiR  864 (910)
                      =|.||+.|-|..|...-             ||+  |.  |..+       ..|.+|..+..-.+|++-++  -++|++-|
T Consensus        38 ~l~vs~~GVG~Ita~Tpm~e~aI~~aL~g~Y~l--Rs--GM~t-------~~G~iv~~fqA~k~d~V~lvi~G~kgtV~r  106 (191)
T PRK10718         38 STKVSEQGVGEITASTPLQEQAIADALDGDYRL--RS--GMKT-------ANGNVVRFFEAMKGDQVAMVINGQQGTVSR  106 (191)
T ss_pred             CEEEECCCCCCCCCCCCCCHHHHHHHHCCCCEE--CC--CCEE-------CCCEEEEEEEECCCCEEEEEEECCCCEEEE
T ss_conf             338842653431358836789999874897366--36--5521-------498499988541788189999668863999


Q ss_pred             EECCC
Q ss_conf             99010
Q gi|254780182|r  865 VPVNE  869 (910)
Q Consensus       865 ~~v~~  869 (910)
                      +.|.+
T Consensus       107 I~V~D  111 (191)
T PRK10718        107 IDVLD  111 (191)
T ss_pred             EEEEC
T ss_conf             99855


No 88 
>PRK13695 putative NTPase; Provisional
Probab=48.37  E-value=14  Score=15.32  Aligned_cols=46  Identities=28%  Similarity=0.617  Sum_probs=32.9

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHCC--CCCHH--HHHHHHCCCCCEEEE
Q ss_conf             999924644352899999999998716--65014--458730374655799
Q gi|254780182|r  265 QIVVTEIPYQVNKAAMLEKIAELVREK--RIVDI--ADLRDESDRQGYRVV  311 (910)
Q Consensus       265 ~ivItEiPY~vnk~~lie~Ia~lv~~~--ki~gI--~dirDeSdr~giRiv  311 (910)
                      .|.||=-| ++.|+.|+.||.+...+.  ++.|.  ..+|+...|-|..++
T Consensus         5 kI~iTG~P-GvGKTTli~Kv~~~L~~~g~~v~GF~T~Evre~G~R~GF~vv   54 (174)
T PRK13695          5 RIGITGMP-GVGKTTLVLKIAELLAREGYKVGGFITEEVREGGKRIGFKII   54 (174)
T ss_pred             EEEEECCC-CCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCEEEEEEEE
T ss_conf             99987899-988999999999998636961746995256038828505999


No 89 
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=48.09  E-value=14  Score=15.42  Aligned_cols=61  Identities=13%  Similarity=0.181  Sum_probs=38.2

Q ss_pred             HHHHCCCCCCCCCCH-HHHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCCCCCCHHHHHHHHHHHCC
Q ss_conf             863137540008973-678999999987899999811----340425566436688704789999997122
Q gi|254780182|r   37 ILGRAIPDLRDGLKP-VHRRILFGMMQMGVEWNKKYV----KCARISGEVMGKYHPHGNAAIYDALARMAQ  102 (910)
Q Consensus        37 I~~RAlPd~rDGlKp-v~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gkyHPHGd~siy~a~v~maq  102 (910)
                      -|||+|=+- .+..| ..+||+=++.+||..||..-+    +..+++|-+++.+.    ...|..+++-.+
T Consensus        17 TVSrvLN~~-~~Vs~~Tr~rV~~aa~eLgY~Pn~~Ar~L~~~~s~~Igviv~~~~----~~f~~~~~~~i~   82 (342)
T PRK10727         17 TVSRVINNS-PKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVS----DPFFGAMVKAVE   82 (342)
T ss_pred             HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCEEEEEECCCC----CCHHHHHHHHHH
T ss_conf             999997797-999999999999999993998588888650177887999958775----421467788999


No 90 
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245   This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=47.36  E-value=16  Score=14.83  Aligned_cols=30  Identities=13%  Similarity=0.171  Sum_probs=11.3

Q ss_pred             CCCCCCCCCCCCCE-EEEECCCCEEEEEEEEC
Q ss_conf             10554451568738-89808998799999835
Q gi|254780182|r  868 NEIRIASRATKGVV-IFSTAKDERVVSVERIR  898 (910)
Q Consensus       868 ~~I~~~gR~a~GV~-i~~L~~~D~Vv~va~i~  898 (910)
                      +-|=.||=-|..-. ++.--. ++|.|+|.|.
T Consensus       296 DAI~LTGGlAys~~f~v~~I~-~~v~fIAPv~  326 (353)
T TIGR02707       296 DAIILTGGLAYSKYFFVSEIR-KRVSFIAPVL  326 (353)
T ss_pred             EEEEECCCHHCCCCHHHHHHH-HCCCEECCEE
T ss_conf             689854601306204558776-1332103668


No 91 
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=47.13  E-value=16  Score=14.81  Aligned_cols=92  Identities=12%  Similarity=0.229  Sum_probs=42.2

Q ss_pred             EEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEE--EEECCCCCEEEEEECCCEEEE-----EEHHHCCCCCCCCC
Q ss_conf             99947991898423686204777227866158985788--896189826999936985999-----75876235478665
Q gi|254780182|r  649 VFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILS--VETCTQENDILLTTKLGQCVR-----FPISAIRVFAGRNS  721 (910)
Q Consensus       649 vl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~--v~~~~~~~~Iil~T~~G~~lr-----F~~~evr~~~GR~a  721 (910)
                      .+.|++|.++-..+  |...+-.-..-++..++-++..  ...++.....++++..|+...     |..++....  -.-
T Consensus      1111 ~~F~R~G~~~i~~~--~~~~k~~~~~~~~V~~~Q~V~KG~~l~~~~~Ge~~v~~~~G~~~~~~~~f~i~~ee~~~--~V~ 1186 (1552)
T TIGR02386      1111 ILFSRKGSLKILRY--FQELKTVEISELKVLDSQKVIKGENLVVDKKGEEIVVSEEGRIKIEDKKFLIVEEEEVV--PVK 1186 (1552)
T ss_pred             EEEEECCEEEEEEE--ECHHHEEECCEEEEECCCEEECCCEEEECCCCCEEEECCCCEEEEECCCEEEECCCEEE--ECC
T ss_conf             57863260788762--00100110012564057355337136765888767707888788505857764032156--426


Q ss_pred             CCEEEEECCCCCEEEEEEEECCCC
Q ss_conf             535767528998699989733666
Q gi|254780182|r  722 VGVRGISLAKGDQVISMAIVLHAD  745 (910)
Q Consensus       722 ~GVkgIkL~~~D~Vv~~~vi~~~~  745 (910)
                      .|+ -|....||.|-...++...|
T Consensus      1187 ~G~-~i~V~~g~~V~~G~~~aefD 1209 (1552)
T TIGR02386      1187 LGT-KILVEDGDAVKEGQRIAEFD 1209 (1552)
T ss_pred             CCC-EEEEECCCCCCCCCEEEEEC
T ss_conf             566-88861586205887578844


No 92 
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.00  E-value=16  Score=14.79  Aligned_cols=64  Identities=16%  Similarity=0.242  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHH----HHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             799999989999999998875304989----9999999989999984056883310013434530101456781899907
Q gi|254780182|r  469 GRDDIRNELNSLGIEIKECLDILSSRS----RLLGIIKQELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSH  544 (910)
Q Consensus       469 E~~kl~~E~~eL~~~I~~l~~IL~s~~----~l~~iI~~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~  544 (910)
                      |...+++...+|..+++.|++-++|-.    .....|-++|..++.--|.-                -+.-+-++||++.
T Consensus        58 e~~s~Q~~~~~L~~ev~~~~~~~~s~~~~~~t~~~~ie~~l~~l~~~aG~v----------------~V~G~Gl~ITi~d  121 (247)
T COG3879          58 ELRSLQKKVNTLAAEVEDLENKLDSVRRSVLTDDAALEDRLEKLRMLAGSV----------------PVTGPGLVITIDD  121 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----------------CCCCCCEEEEECC
T ss_conf             989999999999999999999998877767769999999999998885557----------------7747857999658


Q ss_pred             CCEE
Q ss_conf             9705
Q gi|254780182|r  545 LGYV  548 (910)
Q Consensus       545 ~GyI  548 (910)
                      .||.
T Consensus       122 ~~~~  125 (247)
T COG3879         122 PGYS  125 (247)
T ss_pred             CCCC
T ss_conf             9878


No 93 
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=46.18  E-value=16  Score=14.69  Aligned_cols=28  Identities=29%  Similarity=0.296  Sum_probs=13.8

Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             11561314788708877697201357899978999
Q gi|254780182|r  105 SLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAA  139 (910)
Q Consensus       105 ~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~  139 (910)
                      .+|--|...-..||.       |....|.+|+.+.
T Consensus       151 ~lrk~ll~~~~~yG~-------a~~~LE~~L~~le  178 (569)
T PRK04778        151 ELRKSLLANSFSFGP-------ALDELEKQLENLE  178 (569)
T ss_pred             HHHHHHHHHCCCCCH-------HHHHHHHHHHHHH
T ss_conf             999999985221033-------6999999999999


No 94 
>pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation.
Probab=46.17  E-value=16  Score=14.69  Aligned_cols=20  Identities=25%  Similarity=0.132  Sum_probs=9.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHH
Q ss_conf             63000299999999999999
Q gi|254780182|r  348 KPERFTLIGILKAFVAFREE  367 (910)
Q Consensus       348 ~P~~l~Lk~iL~~fi~hR~e  367 (910)
                      +|.+......+..|+.|-.+
T Consensus       301 k~~V~~~~~~i~~~l~~~~~  320 (559)
T pfam06160       301 KKFVEKNIDKLTDFLEHARE  320 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999857889999999999


No 95 
>pfam07798 DUF1640 Protein of unknown function (DUF1640). This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Probab=46.11  E-value=16  Score=14.69  Aligned_cols=38  Identities=29%  Similarity=0.395  Sum_probs=19.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             36999999999878999988879999998999999999887530
Q gi|254780182|r  448 YLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDIL  491 (910)
Q Consensus       448 ~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL  491 (910)
                      .++..+|+.=|||-      ||+-.+++|......+|.++..=+
T Consensus        99 ei~k~~a~~klDlN------leK~riree~~~~e~ki~e~~~kI  136 (177)
T pfam07798        99 EIDKVTAGVRLDLN------LEKGRIREELAEQELKIKETDTKI  136 (177)
T ss_pred             HHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99986152576545------552077899987999999999899


No 96 
>cd04618 CBS_pair_5 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=45.98  E-value=13  Score=15.65  Aligned_cols=69  Identities=17%  Similarity=0.286  Sum_probs=45.6

Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCE--EEEHHHHH--------HHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCC-
Q ss_conf             00897367899999998789999981--13404255--------66436688704789999997122011156131478-
Q gi|254780182|r   46 RDGLKPVHRRILFGMMQMGVEWNKKY--VKCARISG--------EVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQ-  114 (910)
Q Consensus        46 rDGlKpv~Rrily~m~~~~~~~~~~~--~K~a~ivg--------~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~-  114 (910)
                      -|+--|| ++-+++|.+.|...- |-  .+..+.||        +++--.|-|-+.|+|||.-.|-|.=.-|.|++|.. 
T Consensus         6 ~D~~l~v-k~Af~al~~ngi~~a-plWds~~~~fvGmLt~~DfI~il~lv~i~P~~sL~da~~~l~~~~ihrlPvid~~~   83 (98)
T cd04618           6 FDTKLPV-KKAFNALVENGIRSA-PLWDSRKQQFVGMLTITDFILILRLVSIHPERSLFDAALLLLKNKIHRLPVIDPST   83 (98)
T ss_pred             EECCCCH-HHHHHHHHHCCCEEE-EEECCCCCEEEEEEEHHHHHHHHHHEECCCCCHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             9489758-999999998692699-98728876788886479999887624448761299999999867875052164799


Q ss_pred             CC
Q ss_conf             87
Q gi|254780182|r  115 GN  116 (910)
Q Consensus       115 Gn  116 (910)
                      ||
T Consensus        84 ~~   85 (98)
T cd04618          84 GT   85 (98)
T ss_pred             CC
T ss_conf             96


No 97 
>COG2949 SanA Uncharacterized membrane protein [Function unknown]
Probab=45.21  E-value=14  Score=15.24  Aligned_cols=151  Identities=25%  Similarity=0.311  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHC--CCCCCCHHHHH-----HHHHHHCCCHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             67899999998789999981134042556643--66887047899-----999971220111561314788708877697
Q gi|254780182|r   52 VHRRILFGMMQMGVEWNKKYVKCARISGEVMG--KYHPHGNAAIY-----DALARMAQDWSLRLLLIEGQGNFGSVDGDP  124 (910)
Q Consensus        52 v~Rrily~m~~~~~~~~~~~~K~a~ivg~v~g--kyHPHGd~siy-----~a~v~maq~~~~r~plidg~GnfGs~dgd~  124 (910)
                      .+|-|-|+  --++.++.+-.--+|-||-|+|  ||-+.|---.|     +|.+.+=+-=..+|.|+.|.  .++..-+.
T Consensus        35 ~dr~i~~~--t~~~i~~~~~~lP~r~vgvVLGtsky~~~g~~N~yy~~Ri~aA~~ly~~gKV~~LLlSGD--N~~~sYnE  110 (235)
T COG2949          35 ADRWISWA--TAGLIYDDIQDLPARQVGVVLGTSKYLAKGPPNRYYTYRIDAAIALYKAGKVNYLLLSGD--NATVSYNE  110 (235)
T ss_pred             HHHHHHHH--HCCCCCCCHHHCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEEECC--CCCCCCCC
T ss_conf             87887765--347621685458862048997223002479955768999999999986477049998168--77534654


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHC-CCCCCC----CEECCCCCCCCCEECCCCCCC---CHHCCCCCE-EEHHHHCCC----
Q ss_conf             2013578999789999998630-768405----330689885485034322732---110167610-101331789----
Q gi|254780182|r  125 PAAERYTECRLQKAAHFLLDDL-GKDTVD----FRPNYDGSFQEPVVLCARYPN---VLVNGGGGI-AVGMATNIP----  191 (910)
Q Consensus       125 ~AA~RYte~rl~~~~~~~l~~i-~~~tv~----~~~n~D~~~~EP~vlP~~~P~---lL~nG~~GI-AvGmaTnip----  191 (910)
                      |-+|+=---++---++.|+-|- .--|.|    -..-||-..  =++.--+|-+   |.+--.-|| |+|+++-=|    
T Consensus       111 p~tM~kdL~~~GVp~~~i~lDyAGFrTLDSvvRA~kVF~~~~--ftIItQ~FHceRAlfiA~~~gIdAic~~ap~p~~~~  188 (235)
T COG2949         111 PRTMRKDLIAAGVPAKNIFLDYAGFRTLDSVVRARKVFGTND--FTIITQRFHCERALFIARQMGIDAICFAAPDPEGRS  188 (235)
T ss_pred             HHHHHHHHHHCCCCHHHEEECCCCCCHHHHHHHHHHHCCCCC--EEEEECCCCCHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf             589999999839988890320037417898998998707672--799820123488999999829754786589944467


Q ss_pred             --CCCHHHHHHHHHHHHHC
Q ss_conf             --85478999999887618
Q gi|254780182|r  192 --THNLGEVVDGCVAVIDN  208 (910)
Q Consensus       192 --pHNl~Ev~~a~~~~i~~  208 (910)
                        +--++|+..-+.|++|-
T Consensus       189 ~~~vrlRE~~ARv~Av~D~  207 (235)
T COG2949         189 GLSVRLREFLARVKAVLDL  207 (235)
T ss_pred             CCEEHHHHHHHHHHHHHHH
T ss_conf             7020799999888787410


No 98 
>pfam05400 FliT Flagellar protein FliT. This family contains several bacterial flagellar FliT proteins. The flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium.
Probab=45.18  E-value=17  Score=14.58  Aligned_cols=42  Identities=12%  Similarity=0.181  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             999999988753049899999999989999984056883310
Q gi|254780182|r  479 SLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI  520 (910)
Q Consensus       479 eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I  520 (910)
                      +......-++.||.++.+++.++...|.++.+.++.-||..-
T Consensus        60 ~~~~~~~lL~~IL~nda~IR~Ll~prl~~Ls~li~q~~~q~~  101 (109)
T pfam05400        60 EQEQKRELLQKILDNEAEIKDLLQPRLDELSQLIGQSRRQQS  101 (109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999987999999889999999999988788889


No 99 
>pfam01255 Prenyltransf Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase.
Probab=45.00  E-value=17  Score=14.55  Aligned_cols=64  Identities=11%  Similarity=0.084  Sum_probs=32.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             4523699999999987899998887999999899999999988753049899999999989999984056883
Q gi|254780182|r  445 GTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRR  517 (910)
Q Consensus       445 ~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RR  517 (910)
                      ++|+=+....+++.++=.+.|.        .+..++.+ -.---.++++.+.+-.-+++.+.++.+.-...++
T Consensus        50 EN~~R~~~Ev~~L~~l~~~~l~--------~~~~~~~~-~~iki~~iG~~~~Lp~~l~~~i~~~e~~T~~n~~  113 (222)
T pfam01255        50 ENWKRPKEEVDFLMELLEEKLR--------RLLEDLHK-NGVRVRVIGDLSLLPEDLRKAIEDAEEATKNNTG  113 (222)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHH--------HHHHHHHH-CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             7549998999999999999999--------99999998-6938999526556898999999999997157885


No 100
>pfam02650 HTH_WhiA Sporulation Regulator WhiA C terminal domain. This domain is found at the C terminal of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure. WhiA is a distant homologue of LAGLIDADG homing endonucleases.
Probab=44.68  E-value=17  Score=14.52  Aligned_cols=38  Identities=18%  Similarity=0.323  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCH
Q ss_conf             89999999999871665014458730374655799994798877
Q gi|254780182|r  277 KAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASA  320 (910)
Q Consensus       277 k~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~  320 (910)
                      ...+.+.+.++.+.-.++.  -+   ..|. =+.++.+|+..+.
T Consensus        41 ~~~~a~~l~~~l~~~~~~~--k~---~~r~-~~~ivYlK~~e~I   78 (191)
T pfam02650        41 DEEFAEQLQKLLNEFGLNA--KI---IERR-NKYVVYLKDAEQI   78 (191)
T ss_pred             CHHHHHHHHHHHHHCCCCC--EE---EEEC-CCEEEEECCHHHH
T ss_conf             8999999999999779984--69---8876-9569998579999


No 101
>PRK05595 replicative DNA helicase; Provisional
Probab=43.86  E-value=18  Score=14.42  Aligned_cols=23  Identities=22%  Similarity=0.450  Sum_probs=16.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98999999999899999840568
Q gi|254780182|r  493 SRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       493 s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      ++......|-..|+.+.+.++-|
T Consensus       331 ~r~~ev~~isr~LK~lAkel~ip  353 (444)
T PRK05595        331 SRQQEVSEISRSIKALAKEMECP  353 (444)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             89999999999999999996997


No 102
>KOG4248 consensus
Probab=43.84  E-value=18  Score=14.42  Aligned_cols=34  Identities=29%  Similarity=0.294  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCC-CCCCEECCCCCC
Q ss_conf             3578999789999998630768-405330689885
Q gi|254780182|r  128 ERYTECRLQKAAHFLLDDLGKD-TVDFRPNYDGSF  161 (910)
Q Consensus       128 ~RYte~rl~~~~~~~l~~i~~~-tv~~~~n~D~~~  161 (910)
                      ||--|+||.+|-+.++.++... |++|..|-+|++
T Consensus       268 ~r~~~~r~~~fl~~~~e~ln~~~t~~~n~nh~g~e  302 (1143)
T KOG4248         268 LRRLESRLQPFLQRYYEVLNAAATTDYNNNHEGRE  302 (1143)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCHH
T ss_conf             99999988899999999861352022114654304


No 103
>COG2312 Erythromycin esterase homolog [General function prediction only]
Probab=43.69  E-value=7.2  Score=17.86  Aligned_cols=48  Identities=33%  Similarity=0.515  Sum_probs=36.2

Q ss_pred             EEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCC--CCCCCCHHHH
Q ss_conf             340425566436688704789999997122011156131478870887--7697201357
Q gi|254780182|r   73 KCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSV--DGDPPAAERY  130 (910)
Q Consensus        73 K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs~--dgd~~AA~RY  130 (910)
                      +-+|||+  +|.=- ||+..+|.+=+||-+.      ||+-+| |+++  .-|.|.+++-
T Consensus        43 ~~~RiV~--LGE~s-HGt~e~~~~k~rm~r~------Lvee~G-f~~iA~EA~~~d~~av   92 (405)
T COG2312          43 TDARIVL--LGEPS-HGTGEFFAFKARMFRA------LVEELG-FRAIAFEADFPDAQAV   92 (405)
T ss_pred             CCCEEEE--ECCCC-CCCCHHHHHHHHHHHH------HHHHHC-CCEEEECCCCHHHHHH
T ss_conf             6773898--43777-7740789999999999------999838-6268741683778889


No 104
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.46  E-value=18  Score=14.37  Aligned_cols=14  Identities=21%  Similarity=0.506  Sum_probs=6.5

Q ss_pred             CCCHHHHHHHHHHH
Q ss_conf             88778999999976
Q gi|254780182|r  317 GASADVILNQLYRY  330 (910)
Q Consensus       317 ~~~~~~vln~Lyk~  330 (910)
                      +...+.|-+-||+.
T Consensus        47 gi~lN~VRk~LY~L   60 (178)
T PRK06266         47 GIKLNTVRKILYKL   60 (178)
T ss_pred             CCCHHHHHHHHHHH
T ss_conf             99789999999999


No 105
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=42.39  E-value=18  Score=14.25  Aligned_cols=82  Identities=23%  Similarity=0.355  Sum_probs=41.7

Q ss_pred             HHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Q ss_conf             999861899789878776312697889999974022111222344523699999999987-8999988879999998999
Q gi|254780182|r  401 VRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILEL-RLARLTGLGRDDIRNELNS  479 (910)
Q Consensus       401 I~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdM-rL~rLt~LE~~kl~~E~~e  479 (910)
                      |+.||.  |++..+.+|-.|.                         +   ..-.+.|+++ .-+|-...+.+.|+.|...
T Consensus         4 ik~IRe--Npe~v~~~lkkR~-------------------------~---~~~id~il~lD~~rr~l~~e~e~Lr~erN~   53 (422)
T PRK05431          4 IKLIRE--NPDAVKEKLAKRG-------------------------D---PLDVDELLELDEERRELQTETEELQAERNA   53 (422)
T ss_pred             HHHHHH--CHHHHHHHHHHCC-------------------------C---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             789874--9999999998659-------------------------8---451999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHCCHHH---HHHHHHHHHHHHHHHC
Q ss_conf             99999988753049899---9999999899999840
Q gi|254780182|r  480 LGIEIKECLDILSSRSR---LLGIIKQELLSVKDEL  512 (910)
Q Consensus       480 L~~~I~~l~~IL~s~~~---l~~iI~~EL~eik~ky  512 (910)
                      +.++|..+.+-=.+.+.   ..+-+++++.++.++.
T Consensus        54 iSK~Ig~~kk~g~~~~~l~~~~~~lk~~i~~le~~~   89 (422)
T PRK05431         54 LSKEIGQAKAKGEDAEELIAEVKELKEEIKALEAEL   89 (422)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999987489779999999999999999999999


No 106
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=42.22  E-value=18  Score=14.23  Aligned_cols=21  Identities=29%  Similarity=0.561  Sum_probs=17.7

Q ss_pred             CCCHHHHHHHHHH-HHCCCCCC
Q ss_conf             8973678999999-98789999
Q gi|254780182|r   48 GLKPVHRRILFGM-MQMGVEWN   68 (910)
Q Consensus        48 GlKpv~Rrily~m-~~~~~~~~   68 (910)
                      +|-|.||||+... +.|||.+.
T Consensus        25 ~lsp~qRrivh~La~~lGL~h~   46 (60)
T cd02639          25 SLSPAERRIVHLLASRLGLNHV   46 (60)
T ss_pred             CCCHHHHHHHHHHHHHCCCCEE
T ss_conf             9999999999999988199204


No 107
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=42.17  E-value=18  Score=14.22  Aligned_cols=53  Identities=19%  Similarity=0.450  Sum_probs=31.2

Q ss_pred             HHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCC----CHHCCCCCCCCCCC
Q ss_conf             8999999987899999811340425566436688704789999997122----01115613147887
Q gi|254780182|r   54 RRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQ----DWSLRLLLIEGQGN  116 (910)
Q Consensus        54 Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq----~~~~r~plidg~Gn  116 (910)
                      ..+.--||+-|+-+     +.-++|     .|-|+-.+++-++=|-...    -|..+|||.|+.+-
T Consensus       155 ~~~F~~L~~kGliy-----r~~~~V-----~wcp~~~Tals~~EV~~~~~~~~~~~ikf~l~~~~~~  211 (877)
T PRK05729        155 REVFVRLYEKGLIY-----RGKRLV-----NWDPKLQTALSDLEVEYKEVKGKLWHIRYPLADGSDY  211 (877)
T ss_pred             HHHHHHHHHCCCEE-----ECCEEC-----CCCCCCCCHHHHHHHHCCCCCCCEEEEECCCCCCCCE
T ss_conf             99999999889978-----413123-----6688778843567873245667338984132478874


No 108
>cd04585 CBS_pair_ACT_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in  the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms.  They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The i
Probab=42.14  E-value=18  Score=14.22  Aligned_cols=75  Identities=19%  Similarity=0.269  Sum_probs=35.1

Q ss_pred             CCCCCCCCCCHH----HHHHHHHHHHCCCCCC---CCEEEEHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHCCCCC
Q ss_conf             375400089736----7899999998789999---9811340425566436688---70478999999712201115613
Q gi|254780182|r   41 AIPDLRDGLKPV----HRRILFGMMQMGVEWN---KKYVKCARISGEVMGKYHP---HGNAAIYDALARMAQDWSLRLLL  110 (910)
Q Consensus        41 AlPd~rDGlKpv----~Rrily~m~~~~~~~~---~~~~K~a~ivg~v~gkyHP---HGd~siy~a~v~maq~~~~r~pl  110 (910)
                      ++|=+-+| |++    +|-|+.+|...+...+   ..+.....-|+++|- -+|   +.|.++++|+-.|.+.---+.|.
T Consensus        26 ~lpVvd~~-~lvGiit~~Di~~~~~~~~~~~~~~~~~~~~~~~~v~~im~-~~~~tv~~~~~l~~a~~~m~~~~i~~lpV  103 (122)
T cd04585          26 RLPVVDRG-KLVGIVTDRDLKLASPSKATTLDIWELYYLLSKIKVSDIMT-RDPITVSPDASVEEAAELMLERKISGLPV  103 (122)
T ss_pred             EEEEEECC-EEEEEEEHHHHHHHHHCCCCCCCHHHHHCCCCCCCHHHHCC-CCCEEEECCCCHHHHHHHHHHCCCCEEEE
T ss_conf             89999899-99999988999987750465533355421203889999577-89889938866999999998759878999


Q ss_pred             CCCCCCC
Q ss_conf             1478870
Q gi|254780182|r  111 IEGQGNF  117 (910)
Q Consensus       111 idg~Gnf  117 (910)
                      +|.+|.+
T Consensus       104 vd~~g~l  110 (122)
T cd04585         104 VDDQGRL  110 (122)
T ss_pred             EECCCEE
T ss_conf             9589989


No 109
>pfam04849 HAP1_N HAP1 N-terminal conserved region. This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34.
Probab=42.02  E-value=19  Score=14.20  Aligned_cols=45  Identities=18%  Similarity=0.228  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             999999899999999988753049899999999989999984056
Q gi|254780182|r  470 RDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDT  514 (910)
Q Consensus       470 ~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd  514 (910)
                      ...++...+.+..+-+++...|...+..-..+..||.+++++|..
T Consensus       244 i~dLq~r~k~l~~EnEEL~~~L~~~ke~Q~~L~~El~el~~rY~E  288 (307)
T pfam04849       244 IVDLQKKCKSYALENEELQQHLAAAKDAQRQLQAELQELQDKYAE  288 (307)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999988548999999999899899999999999999999


No 110
>pfam10168 Nup88 Nuclear pore component. Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells.
Probab=41.93  E-value=19  Score=14.19  Aligned_cols=11  Identities=18%  Similarity=0.081  Sum_probs=4.2

Q ss_pred             HHHHHHHHHHH
Q ss_conf             98887789999
Q gi|254780182|r  380 ARDRAHVLVGL  390 (910)
Q Consensus       380 a~~R~HILeGL  390 (910)
                      .++|.++|...
T Consensus       563 i~kRV~~L~~q  573 (717)
T pfam10168       563 FQRRVKLLQLQ  573 (717)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 111
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=41.64  E-value=19  Score=14.16  Aligned_cols=54  Identities=20%  Similarity=0.289  Sum_probs=36.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             7898547899999988761877688888863458668874434475889999870
Q gi|254780182|r  189 NIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYAT  243 (910)
Q Consensus       189 nippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~t  243 (910)
                      ..||||+.--.-.+=+++-+|+. .+....++..-||+...+=.=-..+.+.|+.
T Consensus         1 ~~~p~~~eAE~~vLG~il~~~~~-~~~i~~~l~~~dFy~~~H~~IF~a~~~l~~~   54 (435)
T COG0305           1 RLPPQDIEAEQAVLGGILLDPDA-IERVSERLRPEDFYRPAHRLIYQAILDLYGQ   54 (435)
T ss_pred             CCCCCCHHHHHHHHHHHHCCHHH-HHHHHHHCCHHHCCCHHHHHHHHHHHHHHHC
T ss_conf             98997779999986654048888-9999972685320767899999999999866


No 112
>cd04600 CBS_pair_HPP_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is uncertain, but they are thought to be transporters. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=41.63  E-value=19  Score=14.16  Aligned_cols=28  Identities=14%  Similarity=0.296  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHCCCHHCCCCCCCCCCCC
Q ss_conf             4789999997122011156131478870
Q gi|254780182|r   90 NAAIYDALARMAQDWSLRLLLIEGQGNF  117 (910)
Q Consensus        90 d~siy~a~v~maq~~~~r~plidg~Gnf  117 (910)
                      |+++.+|+-.|.+.--.++|.+|.+|.+
T Consensus        10 ~~tl~~a~~~m~~~~~~~lpVvd~~g~l   37 (124)
T cd04600          10 DTSLEEAWALLRRHRIKALPVVDGDRRL   37 (124)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEEECCCCE
T ss_conf             3979999999997299789999569808


No 113
>COG4939 Major membrane immunogen, membrane-anchored lipoprotein [Function unknown]
Probab=41.23  E-value=19  Score=14.11  Aligned_cols=47  Identities=21%  Similarity=0.208  Sum_probs=35.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHH-----HHHHHHHHHHHHHHCCCCCCC
Q ss_conf             15613147887088776972013578-----999789999998630768405
Q gi|254780182|r  106 LRLLLIEGQGNFGSVDGDPPAAERYT-----ECRLQKAAHFLLDDLGKDTVD  152 (910)
Q Consensus       106 ~r~plidg~GnfGs~dgd~~AA~RYt-----e~rl~~~~~~~l~~i~~~tv~  152 (910)
                      -.|-.-++.|||-|-|.|-+-+|.|-     +--++.+|..|++--+.+-||
T Consensus        62 ~~ydy~~k~G~~Ks~DAdy~~~mk~~~g~gp~~~f~~laD~Lve~q~p~~Vd  113 (147)
T COG4939          62 CTYDYRDKKGNIKSDDADYAGEMKYMKGQGPVQGFSTLADKLVEVQDPNEVD  113 (147)
T ss_pred             EEEEEECCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             8855064778736653336777777416377899999999987248945055


No 114
>PRK08082 consensus
Probab=41.12  E-value=19  Score=14.09  Aligned_cols=22  Identities=27%  Similarity=0.465  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             8999999999899999840568
Q gi|254780182|r  494 RSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       494 ~~~l~~iI~~EL~eik~kygd~  515 (910)
                      +......|-..|+.+.+.++-|
T Consensus       335 r~~ev~~isr~LK~lAkel~ip  356 (453)
T PRK08082        335 RQQEVSEISRTLKALARELEVP  356 (453)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999999999999999996997


No 115
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=40.38  E-value=17  Score=14.51  Aligned_cols=16  Identities=38%  Similarity=0.762  Sum_probs=7.4

Q ss_pred             HHHHHHHHCCCEEEEE
Q ss_conf             8999987012038999
Q gi|254780182|r  236 GIKNAYATGRGSIVIR  251 (910)
Q Consensus       236 ~i~~~y~tGrG~i~iR  251 (910)
                      -|.+||+.||||+++-
T Consensus        39 Rl~~Afe~grgsVR~L   54 (75)
T cd04469          39 RLKTAFESGRGSVRVL   54 (75)
T ss_pred             HHHHHHHCCCCCEEEE
T ss_conf             9999976489839999


No 116
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=40.13  E-value=20  Score=13.98  Aligned_cols=23  Identities=17%  Similarity=0.517  Sum_probs=12.9

Q ss_pred             CCCEEEEECCCCCEEEEEEEECC
Q ss_conf             55357675289986999897336
Q gi|254780182|r  721 SVGVRGISLAKGDQVISMAIVLH  743 (910)
Q Consensus       721 a~GVkgIkL~~~D~Vv~~~vi~~  743 (910)
                      ..|++|.-.-++|++||.....+
T Consensus       200 ~~~i~GaPVvd~dk~vGiit~~d  222 (294)
T COG2524         200 EKGIRGAPVVDDDKIVGIITLSD  222 (294)
T ss_pred             HCCCCCCCEECCCCEEEEEEHHH
T ss_conf             72866785102894589998899


No 117
>pfam04637 Herpes_pp85 Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25). This family includes UL25 proteins from HCMV, as well as U14 proteins from HHV 6 and HHV7. These 85 kD phosphoproteins appear to act as structural antigens, but their precise function is otherwise unknown.
Probab=39.82  E-value=20  Score=13.94  Aligned_cols=180  Identities=21%  Similarity=0.284  Sum_probs=98.9

Q ss_pred             CCEECCCCCCCCHHCCCCCEEEHHHHCC-----CCCCHHHHHHHHHHH--HHCCCCCHHHHHHHCCCCCCCCCCCCCCHH
Q ss_conf             8503432273211016761010133178-----985478999999887--618776888888634586688744344758
Q gi|254780182|r  163 EPVVLCARYPNVLVNGGGGIAVGMATNI-----PTHNLGEVVDGCVAV--IDNPDIDLDALMEIIRGPDFPTGAVILGRT  235 (910)
Q Consensus       163 EP~vlP~~~P~lL~nG~~GIAvGmaTni-----ppHNl~Ev~~a~~~~--i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~  235 (910)
                      ||++-=+-+=|-+.|| .|+++-|-|.+     ||+ ..-+-.++.-+  -.+.+..-..|+..+--=|.|.|-.   ..
T Consensus        66 ~~VIrl~V~iN~y~ng-~~~L~~m~~~~~~l~~~~~-~~rl~~gL~~L~~a~~~~~~p~~l~~~l~~~~ltdg~~---~~  140 (502)
T pfam04637        66 RPVIRLAVLINHYYNG-KGILRHMRAALKSLMNPPT-MRRLDRGLRRLCRALQDSDNPPDLSESLGDLDLTDGQY---KA  140 (502)
T ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCHH-HHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHH---HH
T ss_conf             9999999999999988-9999999999998629547-89999999887540137987589998726689866899---99


Q ss_pred             HHHHHHHHCCCEEEEEEEEEEEEC---CCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEE
Q ss_conf             899998701203899998865433---67845999924644352899999999998716650144587303746557999
Q gi|254780182|r  236 GIKNAYATGRGSIVIRGVSHIEKT---SGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVI  312 (910)
Q Consensus       236 ~i~~~y~tGrG~i~iR~k~~ie~~---~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivi  312 (910)
                      .++.+|...+ ++-.|-..+.+..   =+. ++.- ...|-=++++.+--.         -+.++|+.+-..+ .+|.+.
T Consensus       141 ~L~~l~~l~~-s~~~~~~~~~~~~y~~Lr~-yN~L-f~~P~ft~~eAv~lY---------~~NL~dLt~~~~~-~l~Llt  207 (502)
T pfam04637       141 ALRTLYRLLK-SLGLRESPELESCYETLRA-YNLL-FKPPRFTTREAVDLY---------AENLADLTQRINR-PLRLLT  207 (502)
T ss_pred             HHHHHHHHHH-HCCCCCCHHHHHHHHHHHH-CCCC-CCCCCCCHHHHHHHH---------HHHHHHHHHHCCC-CCEEEE
T ss_conf             9999999998-6078864567888999865-0001-268764218999999---------9999997652268-860676


Q ss_pred             EECCCCCHHHHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             94798877899999997610110000002455416630002999999999999999999
Q gi|254780182|r  313 ELKRGASADVILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVR  371 (910)
Q Consensus       313 elKr~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~r  371 (910)
                      ..|+.-+++-|+|.++-...+.     ||+.-...     .| ..|..||-++.+.+.-
T Consensus       208 ~~~~~~~~e~vlND~lFLls~~-----nmi~~~~~-----~l-r~LR~wI~~qln~l~e  255 (502)
T pfam04637       208 TIKRSKTPEDVLNDLLFLLSLG-----NMIYRHRR-----EL-RALRKWIVLQLNSLCE  255 (502)
T ss_pred             EECCCCCHHHHHHHHHHHHHHH-----HHHHHHHH-----HH-HHHHHHHHHHHHHHHH
T ss_conf             3068897488898999999888-----89999999-----99-9999999999999999


No 118
>KOG1684 consensus
Probab=39.78  E-value=12  Score=15.99  Aligned_cols=15  Identities=20%  Similarity=0.233  Sum_probs=7.3

Q ss_pred             CHHHHHHHHHHHCCC
Q ss_conf             047899999971220
Q gi|254780182|r   89 GNAAIYDALARMAQD  103 (910)
Q Consensus        89 Gd~siy~a~v~maq~  103 (910)
                      =+-++|-.|+-..++
T Consensus        66 Mv~~~~~~L~~we~s   80 (401)
T KOG1684          66 MVLSIYPKLVEWEKS   80 (401)
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             899889988754027


No 119
>KOG0428 consensus
Probab=39.48  E-value=20  Score=13.90  Aligned_cols=10  Identities=40%  Similarity=0.830  Sum_probs=4.5

Q ss_pred             CCCCCCCCCC
Q ss_conf             4788708877
Q gi|254780182|r  112 EGQGNFGSVD  121 (910)
Q Consensus       112 dg~GnfGs~d  121 (910)
                      -+.|-.||+|
T Consensus       123 ~p~GAlGSlD  132 (314)
T KOG0428         123 KPEGALGSLD  132 (314)
T ss_pred             CCCCCCCCCC
T ss_conf             9887534676


No 120
>PRK05617 enoyl-CoA hydratase; Provisional
Probab=39.39  E-value=19  Score=14.11  Aligned_cols=30  Identities=17%  Similarity=0.318  Sum_probs=18.5

Q ss_pred             HCCCCCEEEHHHHCCCC-CCHHHHHHHHHHH
Q ss_conf             01676101013317898-5478999999887
Q gi|254780182|r  176 VNGGGGIAVGMATNIPT-HNLGEVVDGCVAV  205 (910)
Q Consensus       176 ~nG~~GIAvGmaTnipp-HNl~Ev~~a~~~~  205 (910)
                      +||+.-+..|+||..-| .++.++.+++..+
T Consensus       175 l~~~Da~~~GlA~~~v~s~~~~~l~~~L~~~  205 (356)
T PRK05617        175 ISAADALYAGLADHFVPSADLPAFLDALEAT  205 (356)
T ss_pred             CCHHHHHHCCCCCEECCHHHHHHHHHHHHHC
T ss_conf             6999998749442235874699999999826


No 121
>pfam03131 bZIP_Maf bZIP Maf transcription factor. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Thus, this family is probably related to pfam00170.
Probab=39.28  E-value=20  Score=13.88  Aligned_cols=37  Identities=14%  Similarity=0.245  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99999989999999998875304989999999998999998405
Q gi|254780182|r  470 RDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELD  513 (910)
Q Consensus       470 ~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kyg  513 (910)
                      ...|+.|..+|..++..|+.=       ..-+..|...++.||-
T Consensus        55 ~~~LE~e~~~L~~e~e~Lk~E-------~~~~~~E~d~~k~K~e   91 (95)
T pfam03131        55 RHELEKEKSQLQQQVEQLKQE-------NARLRRERDALKAKYE   91 (95)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999-------9999999999999998


No 122
>cd03677 MM_CoA_mutase_beta Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta heterodimers. For P. shermanni MCM, it is known that only the alpha subunit binds coenzyme B12 and substrates. The role of the beta subunit is unclear. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversib
Probab=39.25  E-value=20  Score=13.87  Aligned_cols=23  Identities=26%  Similarity=0.439  Sum_probs=13.9

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             59999246443528999999999
Q gi|254780182|r  264 EQIVVTEIPYQVNKAAMLEKIAE  286 (910)
Q Consensus       264 ~~ivItEiPY~vnk~~lie~Ia~  286 (910)
                      ..|.|.--+|+-.-+..++.+|-
T Consensus       181 ~~i~idg~~~~~AGAt~vQELA~  203 (424)
T cd03677         181 RAITVDAVPYHNAGATAAQELAY  203 (424)
T ss_pred             EEEEEECHHHHHCCCCHHHHHHH
T ss_conf             07998526687679999999999


No 123
>cd03823 GT1_ExpE7_like This family is most closely related to the GT1 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II).
Probab=39.01  E-value=20  Score=13.84  Aligned_cols=12  Identities=17%  Similarity=0.163  Sum_probs=4.5

Q ss_pred             CCCHHHHHHHHH
Q ss_conf             447588999987
Q gi|254780182|r  231 ILGRTGIKNAYA  242 (910)
Q Consensus       231 I~~~~~i~~~y~  242 (910)
                      |.-.+.+++.|.
T Consensus       148 i~~S~~~~~~~~  159 (359)
T cd03823         148 IAPSRFLLDRYV  159 (359)
T ss_pred             EECCHHHHHHHH
T ss_conf             999999999999


No 124
>COG3253 ywfI Predicted heme peroxidase involved in anaerobic stress response [General function prediction only]
Probab=38.72  E-value=9.2  Score=16.91  Aligned_cols=11  Identities=27%  Similarity=0.093  Sum_probs=5.5

Q ss_pred             CEEEEEECCCC
Q ss_conf             45999924644
Q gi|254780182|r  263 REQIVVTEIPY  273 (910)
Q Consensus       263 k~~ivItEiPY  273 (910)
                      ..-.|.-|+|+
T Consensus       178 yEwvV~~e~dd  188 (230)
T COG3253         178 YEWVVTYEADD  188 (230)
T ss_pred             EEEEEEEECCC
T ss_conf             58999984676


No 125
>KOG2941 consensus
Probab=38.46  E-value=21  Score=13.78  Aligned_cols=30  Identities=20%  Similarity=0.245  Sum_probs=10.7

Q ss_pred             CCCEEEEHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf             9981134042556643668870478999999
Q gi|254780182|r   68 NKKYVKCARISGEVMGKYHPHGNAAIYDALA   98 (910)
Q Consensus        68 ~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v   98 (910)
                      +.|+.+++|.+---+||.- |+.-.|..||-
T Consensus       152 ~h~lV~l~~~~E~~fgk~a-~~nLcVT~AMr  181 (444)
T KOG2941         152 QHPLVRLVRWLEKYFGKLA-DYNLCVTKAMR  181 (444)
T ss_pred             CCCHHHHHHHHHHHHHCCC-CCCHHHHHHHH
T ss_conf             8705889999999861334-32224588899


No 126
>PRK08840 replicative DNA helicase; Provisional
Probab=38.18  E-value=21  Score=13.74  Aligned_cols=23  Identities=26%  Similarity=0.447  Sum_probs=15.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98999999999899999840568
Q gi|254780182|r  493 SRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       493 s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      ++......|-..|+.+.+.++-|
T Consensus       349 ~r~~~i~~isr~lK~lAkel~vp  371 (464)
T PRK08840        349 NRTLEIAEISRSLKALAKELNVP  371 (464)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             36789999999999999996998


No 127
>TIGR01465 cobM_cbiF precorrin-4 C11-methyltransferase; InterPro: IPR006362   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 CobM and CibF precorrin-4 C11-methyltransferase (2.1.1.133 from EC), both as stand-alone enzymes and when CobJ forms part of a bifunctional enzyme. In the aerobic pathway, CobM catalyses the methylation of precorrin-4 at C-11 to yield precorrin-5. The extruded acyl group is then removed in the subsequent step catalysed by CobF. In the anaerobic pathway, CibF catalyses the methylation of cobalt-precorrin-4 to cobalt-precoriin-5 .    Nomenclature note: occasionally precorrin-4 C11-methyltransferase is one of two methyltransferases often referred to as precorrin-3 methylase (the other is precorrin-3 methylase (the other is precorrin-4 C11-methyltransferase, 2.1.1.131 from EC). ; GO: 0046026 precorrin-4 C11-methyltransferase activity, 0009236 cobalamin biosynthetic process.
Probab=38.11  E-value=13  Score=15.57  Aligned_cols=14  Identities=43%  Similarity=0.741  Sum_probs=5.7

Q ss_pred             CHHHHHHHHHHHCC
Q ss_conf             04789999997122
Q gi|254780182|r   89 GNAAIYDALARMAQ  102 (910)
Q Consensus        89 Gd~siy~a~v~maq  102 (910)
                      ||-|||.|+.=+-|
T Consensus        80 GDPsIYGA~~EQ~~   93 (252)
T TIGR01465        80 GDPSIYGAIAEQMQ   93 (252)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             87557766999999


No 128
>pfam10458 Val_tRNA-synt_C Valyl tRNA synthetase tRNA binding arm. This domain is found at the C-terminus of Valyl tRNA synthetases.
Probab=38.02  E-value=21  Score=13.72  Aligned_cols=34  Identities=24%  Similarity=0.174  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             8799999989999999998875304989999999
Q gi|254780182|r  468 LGRDDIRNELNSLGIEIKECLDILSSRSRLLGII  501 (910)
Q Consensus       468 LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI  501 (910)
                      -|..+|..|++.+.++|..++.-|+++.-+.+.=
T Consensus         4 ~E~~RL~Kel~kl~~~i~~~~~kL~N~~Fv~kAP   37 (66)
T pfam10458         4 KERARLEKELAKLQKEIERLQKKLSNPGFVAKAP   37 (66)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCC
T ss_conf             8999899999999999999998778767777098


No 129
>cd04603 CBS_pair_KefB_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=38.01  E-value=15  Score=14.94  Aligned_cols=86  Identities=17%  Similarity=0.133  Sum_probs=52.8

Q ss_pred             HHHHHHHHHH---HCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCC--CCCHHHHHHHHHHHCCCH
Q ss_conf             8777998863---13754000897367899999998789999981134042556643668--870478999999712201
Q gi|254780182|r   30 LTYAINVILG---RAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYH--PHGNAAIYDALARMAQDW  104 (910)
Q Consensus        30 l~Ya~svI~~---RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyH--PHGd~siy~a~v~maq~~  104 (910)
                      |.-|+..+.+   ||+|=|-++.||+-==-+-.|.+  +.++   .-+---|+|+|=+=-  -|-|++++|||-.|.|.-
T Consensus        12 L~~a~~~~~e~~~~~i~VVD~~~k~vG~it~~Dll~--~~~~---~~~~~~V~d~m~~~v~~i~~~~~v~dalr~~~~~~   86 (111)
T cd04603          12 LREAIKMINELGARAVVVVDEENKVLGQVTLSDLLE--IGPN---DYETLKVCEVYIVPVPIVYCDSKVTDLLRIFRETE   86 (111)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCCEEEEEEHHHHHH--HCHH---HHHCCCHHHHHCCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             999999998769976899889996889988999864--3844---55324387751567746389976899999987449


Q ss_pred             HCCCCCCCCCCCC-CCC
Q ss_conf             1156131478870-887
Q gi|254780182|r  105 SLRLLLIEGQGNF-GSV  120 (910)
Q Consensus       105 ~~r~plidg~Gnf-Gs~  120 (910)
                      .-+.|.+|+-|.| |.|
T Consensus        87 ~~~l~VVD~~grlvGiI  103 (111)
T cd04603          87 PPVVAVVDKEGKLVGTI  103 (111)
T ss_pred             CCEEEEECCCCCEEEEE
T ss_conf             98899993899799999


No 130
>cd04597 CBS_pair_DRTGG_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=37.82  E-value=21  Score=13.70  Aligned_cols=69  Identities=14%  Similarity=0.159  Sum_probs=52.0

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCC--CCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCC
Q ss_conf             9736789999999878999998113404255664366--88704789999997122011156131478870
Q gi|254780182|r   49 LKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKY--HPHGNAAIYDALARMAQDWSLRLLLIEGQGNF  117 (910)
Q Consensus        49 lKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gky--HPHGd~siy~a~v~maq~~~~r~plidg~Gnf  117 (910)
                      +-++.+..-|.+...|+.+-.=-....--|+|+|-+-  --+.|.|+.+|+-.|.+.---+.|.+|.+|.+
T Consensus        31 ~G~~n~et~~vL~~f~~~~P~li~~v~~qV~DIm~~~~vti~~~~sl~eA~~lM~e~~i~~LPVVD~~g~l  101 (113)
T cd04597          31 LGEPNPQTRYVLEYLGIEPPILLADVHPRVRDVINRKPVTARPNDPLREALNLMHEHNIRTLPVVDDDGTP  101 (113)
T ss_pred             CCCCCHHHHHHHHHCCCCCCEECCCCCCHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCCEE
T ss_conf             68999899999998499998002156505666313788341999829999999998499878698899939


No 131
>pfam00465 Fe-ADH Iron-containing alcohol dehydrogenase.
Probab=37.75  E-value=21  Score=13.69  Aligned_cols=26  Identities=23%  Similarity=0.157  Sum_probs=11.1

Q ss_pred             EEEHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf             01013317898547899999988761
Q gi|254780182|r  182 IAVGMATNIPTHNLGEVVDGCVAVID  207 (910)
Q Consensus       182 IAvGmaTnippHNl~Ev~~a~~~~i~  207 (910)
                      +-+..-+.+.||---|-++.++..++
T Consensus        51 ~~~~~~~~v~~~p~~~~v~~~~~~~~   76 (312)
T pfam00465        51 IEVVVFDGVEPNPTLEEVDEAAAAAR   76 (312)
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             94999858279999999999999999


No 132
>pfam03266 DUF265 Protein of unknown function, DUF265.
Probab=37.60  E-value=21  Score=13.67  Aligned_cols=45  Identities=27%  Similarity=0.602  Sum_probs=27.8

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHCC--CCCHH--HHHHHHCCCCCEEEE
Q ss_conf             99924644352899999999998716--65014--458730374655799
Q gi|254780182|r  266 IVVTEIPYQVNKAAMLEKIAELVREK--RIVDI--ADLRDESDRQGYRVV  311 (910)
Q Consensus       266 ivItEiPY~vnk~~lie~Ia~lv~~~--ki~gI--~dirDeSdr~giRiv  311 (910)
                      |.||= |.++.|++|+.++++..++.  ++.|.  ..+|+..-|-|..++
T Consensus         2 i~ITG-~pGvGKTTli~kv~~~l~~~~~~v~GF~T~evre~g~R~GF~iv   50 (168)
T pfam03266         2 IFITG-PPGVGKTTLVKKVIELLKSEGVKVGGFYTPEVREGGRRIGFDIV   50 (168)
T ss_pred             EEEEC-CCCCCHHHHHHHHHHHHHHCCCEEEEEEECCEECCCCEEEEEEE
T ss_conf             89978-99988999999999999867970748993021258937899999


No 133
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=37.56  E-value=21  Score=13.67  Aligned_cols=11  Identities=36%  Similarity=0.640  Sum_probs=5.2

Q ss_pred             HHHHHHHCCCC
Q ss_conf             99887618776
Q gi|254780182|r  201 GCVAVIDNPDI  211 (910)
Q Consensus       201 a~~~~i~~p~~  211 (910)
                      -+.+++.+|++
T Consensus       167 LA~aL~~~Pdl  177 (632)
T PRK11147        167 LARALVSNPDV  177 (632)
T ss_pred             HHHHHCCCCCE
T ss_conf             99985689999


No 134
>cd04629 CBS_pair_16 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=37.23  E-value=14  Score=15.28  Aligned_cols=32  Identities=13%  Similarity=0.280  Sum_probs=20.2

Q ss_pred             CHHHHHHHHHHHCCCHHCCCCCCCCCCCC-CCC
Q ss_conf             04789999997122011156131478870-887
Q gi|254780182|r   89 GNAAIYDALARMAQDWSLRLLLIEGQGNF-GSV  120 (910)
Q Consensus        89 Gd~siy~a~v~maq~~~~r~plidg~Gnf-Gs~  120 (910)
                      -|+++++|+-.|++.--...|.+|.+|.+ |-+
T Consensus         8 ~~~tl~~a~~~m~~~~~~~~pVvd~~~~lvGii   40 (114)
T cd04629           8 PDMSVTEAVEKLLKSKISGGPVVDDNGNLVGFL   40 (114)
T ss_pred             CCCCHHHHHHHHHHHCCCEEEEECCCCEEEEEE
T ss_conf             929999999999971997899994899299999


No 135
>cd04617 CBS_pair_4 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=37.22  E-value=14  Score=15.30  Aligned_cols=38  Identities=16%  Similarity=0.293  Sum_probs=21.4

Q ss_pred             HHHHHCCCCC-----CCHHHHHHHHHHHCCCHHCCCCCCCCCCC
Q ss_conf             5566436688-----70478999999712201115613147887
Q gi|254780182|r   78 SGEVMGKYHP-----HGNAAIYDALARMAQDWSLRLLLIEGQGN  116 (910)
Q Consensus        78 vg~v~gkyHP-----HGd~siy~a~v~maq~~~~r~plidg~Gn  116 (910)
                      |+++|-+ +|     +-|.++++|+-.|.+.---+.|.+|..|+
T Consensus        60 V~~iMT~-~P~vvt~~pd~~v~~A~~~M~~~~i~~LPVVd~~~~  102 (118)
T cd04617          60 VGVIMTR-MPNITTTTPEESVLEAAKKLIEHQVDSLPVVEKVDE  102 (118)
T ss_pred             HHHHHCC-CCCEEEECCCCCHHHHHHHHHHCCCCEECEEECCCC
T ss_conf             9998577-997199789993999999999829998567943997


No 136
>pfam11802 CENP-K Centromere-associated protein K. CENP-K is one of seven new CENP-A-nucleosome distal (CAD) centromere components (the others being CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S) that are identified as assembling on the CENP-A nucleosome associated complex, NAC. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. CENP-K is centromere-associated through its interaction with one or more components of the CENP-A NAC.
Probab=37.22  E-value=22  Score=13.63  Aligned_cols=62  Identities=18%  Similarity=0.149  Sum_probs=35.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             23699999999987899998887999999----------------89999999998875304989999999998999998
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRDDIRN----------------ELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKD  510 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~kl~~----------------E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~  510 (910)
                      +-.|+.|- ++|-||.+.||+ |.++.+.                =.++|.+.+.+|+..|+.-+...+.++++|.-.+.
T Consensus        52 l~~sd~q~-~ll~~~~k~Lta-E~~qwqk~~peii~~n~~vL~~lgKeelqk~~~dLe~vLs~vqsk~~~LkedLerEqq  129 (273)
T pfam11802        52 LPESDAQL-SLLIMQMKALTA-EYEQWQKRTPEIISLNEDVLLTLGKEELQKLRQDLEMVLSSVQSKNEKLKEDLEREQQ  129 (273)
T ss_pred             CCCCCCCH-HHHHHHHHHHHH-HHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89764008-999999999999-9999997099567898899999879999999999999999999989999999999999


No 137
>COG1791 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=37.12  E-value=22  Score=13.62  Aligned_cols=117  Identities=15%  Similarity=0.224  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHHHHHHHHH-----HHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCC---------CCCCCCCCCC
Q ss_conf             999998999999999887-----53049899999999989999984056883310013434---------5301014567
Q gi|254780182|r  471 DDIRNELNSLGIEIKECL-----DILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLD---------MEDEDCIVRE  536 (910)
Q Consensus       471 ~kl~~E~~eL~~~I~~l~-----~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~---------i~~EdlI~~E  536 (910)
                      +.+..|+..+.-.-++++     +.++++..+......|+..|..++|-.-+-.+.-....         +-.|-+-.++
T Consensus        17 deia~~l~~i~v~~e~we~~~~~~~~~~~~~i~~a~~~eid~l~~e~Gyk~~Dvvsv~~~~pk~del~akF~~EH~H~d~   96 (181)
T COG1791          17 DEIAPELSKIEVSFERWEATALIKHGAEKEHIIDAYETEIDRLIRERGYKNRDVVSVSPSNPKLDELRAKFLQEHLHTDD   96 (181)
T ss_pred             HHHHHHCCCCEEEHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             67400014534676563302555457524424766898999999861972133798579993289999999998536781


Q ss_pred             CEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCC-----CCCCCC
Q ss_conf             818999079705233100000233456521100014641010113323777399995489399982000-----432244
Q gi|254780182|r  537 DMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWR-----LPIGSP  611 (910)
Q Consensus       537 ~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~-----IP~~sr  611 (910)
                      ++-..+.-.||                                         .-+-+..|++|++.+-.     +|.|  
T Consensus        97 EvRy~vaG~Gi-----------------------------------------F~v~~~d~~~~~i~c~~gDLI~vP~g--  133 (181)
T COG1791          97 EVRYFVAGEGI-----------------------------------------FDVHSPDGKVYQIRCEKGDLISVPPG--  133 (181)
T ss_pred             EEEEEEECCEE-----------------------------------------EEEECCCCCEEEEEECCCCEEECCCC--
T ss_conf             17999936558-----------------------------------------99987999689999835987952898--


Q ss_pred             CCCCCCCEEEEECCCCCCEEEEEEE
Q ss_conf             4565541245453655620025663
Q gi|254780182|r  612 QARGKALINILSLNQGERITTIMPF  636 (910)
Q Consensus       612 ~skG~pi~nll~l~~~E~I~ail~~  636 (910)
                            +...+.|..+-.+.|+--+
T Consensus       134 ------i~HwFtlt~~~~f~AvRlF  152 (181)
T COG1791         134 ------IYHWFTLTESPNFKAVRLF  152 (181)
T ss_pred             ------CEEEEECCCCCCEEEEEEE
T ss_conf             ------4388773679867899976


No 138
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=37.03  E-value=22  Score=13.61  Aligned_cols=58  Identities=17%  Similarity=0.160  Sum_probs=24.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             5236999999999878999988879999998999999999887530498999999999899999840
Q gi|254780182|r  446 TMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDEL  512 (910)
Q Consensus       446 ~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~ky  512 (910)
                      +|+=+....+++.++=        ...++.+.+++.+.--. -.++++...+-+-+.+.+.++.+.=
T Consensus        50 Nw~R~~~EV~~Lm~L~--------~~~l~~~~~~l~~~~ir-i~~iGd~~~Lp~~l~~~i~~~e~~T  107 (229)
T PRK10240         50 NWNRPAQEVSALMELF--------VWALDSEVKSLHRHNVR-LRIIGDTSRFNSRLQERIRKSEALT  107 (229)
T ss_pred             HCCCCHHHHHHHHHHH--------HHHHHHHHHHHHHCCEE-EEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             6499979999999999--------99999999999987948-9996441006758999999999974


No 139
>pfam12552 DUF3741 Protein of unknown function (DUF3741). This domain family is found in eukaryotes, and is approximately 50 amino acids in length.
Probab=36.97  E-value=22  Score=13.60  Aligned_cols=39  Identities=21%  Similarity=0.336  Sum_probs=30.3

Q ss_pred             EEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCC
Q ss_conf             1013317898547899999988761877688888863458668
Q gi|254780182|r  183 AVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDF  225 (910)
Q Consensus       183 AvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDF  225 (910)
                      |-+++|+.-+|+-.|..||+-.+=-|.+    =++++++.|+.
T Consensus         8 ~K~ls~d~~~~~SKEf~DAleiL~snkd----lflk~LQdP~s   46 (46)
T pfam12552         8 AKRLSTDEKLHQSKEFLDALEVLNSNKD----LFLKFLQDPNS   46 (46)
T ss_pred             HCCCCCCCCCCCHHHHHHHHHHHHHCHH----HHHHHHCCCCC
T ss_conf             0014555641210999999999971789----99999708998


No 140
>pfam06838 Alum_res Aluminium resistance protein. This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria.
Probab=36.71  E-value=22  Score=13.57  Aligned_cols=14  Identities=14%  Similarity=0.178  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHCCC
Q ss_conf             67899999998789
Q gi|254780182|r   52 VHRRILFGMMQMGV   65 (910)
Q Consensus        52 v~Rrily~m~~~~~   65 (910)
                      -|.|+|-||++.++
T Consensus        26 Nq~KVL~Af~~~~v   39 (405)
T pfam06838        26 NQLKVLNAFQEHRV   39 (405)
T ss_pred             HHHHHHHHHHHCCC
T ss_conf             99999999998097


No 141
>TIGR00683 nanA N-acetylneuraminate lyase; InterPro: IPR005264    N-acetylneuraminate lyase catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetyl-D-mannosamine. The enzyme plays an important role in the regulation of sialic acid metabolism in bacteria..
Probab=35.98  E-value=22  Score=13.48  Aligned_cols=51  Identities=27%  Similarity=0.388  Sum_probs=37.1

Q ss_pred             CHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             7588999987012038999988654336784599992464435289999999999871665014
Q gi|254780182|r  233 GRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDI  296 (910)
Q Consensus       233 ~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI  296 (910)
                      +-+++.+.|+|            |-... |....||..||+-+.-.-=|++|.+|+...++-++
T Consensus       111 SF~E~~~~Y~~------------II~~~-~G~~M~VY~IP~L~GV~l~~~Q~~~L~~~P~V~~~  161 (294)
T TIGR00683       111 SFEEIKDYYDA------------IIDEA-DGLNMVVYSIPALSGVKLTLDQINELVKLPKVLAL  161 (294)
T ss_pred             CCHHHHHHHHH------------HHHHC-CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             73677778999------------98524-89823787453201212218888887517872145


No 142
>KOG0650 consensus
Probab=35.94  E-value=22  Score=13.47  Aligned_cols=50  Identities=22%  Similarity=0.370  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHCCCC--CCCEEECCCCCCCCCCCCCC------------CCEEEEEECCCEECCCCCCC
Q ss_conf             999899999840568--83310013434530101456------------78189990797052331000
Q gi|254780182|r  501 IKQELLSVKDELDTP--RRTRIVEGLLDMEDEDCIVR------------EDMVVTVSHLGYVKRVPLSV  555 (910)
Q Consensus       501 I~~EL~eik~kygd~--RRT~I~~~~~~i~~EdlI~~------------E~vvV~lS~~GyIKr~~~~~  555 (910)
                      |++-+.---+-|=-|  ||..+.     ++.|+|||+            .--.|.--+.|-++.++++-
T Consensus       347 irErFeRcLDLYL~PR~rK~rln-----iDpe~LiPkLPsp~dLrPFPt~~~lvyrGHtg~Vr~iSvdp  410 (733)
T KOG0650         347 IRERFERCLDLYLAPRVRKMRLN-----IDPESLIPKLPSPKDLRPFPTRCALVYRGHTGLVRSISVDP  410 (733)
T ss_pred             HHHHHHHHHHHHHCCCCCCCEEC-----CCHHHHCCCCCCHHHCCCCCCEEEEEEECCCCEEEEEEECC
T ss_conf             99999986776507201231104-----79778552489833257775000246733577378977657


No 143
>cd04639 CBS_pair_26 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=35.59  E-value=23  Score=13.43  Aligned_cols=40  Identities=20%  Similarity=0.238  Sum_probs=19.8

Q ss_pred             HHHHHCC--CCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCC
Q ss_conf             5566436--688704789999997122011156131478870
Q gi|254780182|r   78 SGEVMGK--YHPHGNAAIYDALARMAQDWSLRLLLIEGQGNF  117 (910)
Q Consensus        78 vg~v~gk--yHPHGd~siy~a~v~maq~~~~r~plidg~Gnf  117 (910)
                      |.++|-+  ..=+-|.++++++-+|.+.-.-+.|.+|.+|.+
T Consensus        58 V~~vM~~~v~tv~~~~~l~~~~~~m~~~~~~~lpVVd~~g~l   99 (111)
T cd04639          58 VRGVMRRDFPTVSPSATLDAVLRLMQQGGAPAVPVVDGSGRL   99 (111)
T ss_pred             HHHHCCCCCEEECCCCCHHHHHHHHHHCCCCEEEEECCCCEE
T ss_conf             576354698799899949999999995899889899579929


No 144
>cd07642 BAR_ASAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP2 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2) is also known as DDEF2 (Development and Differentiation Enhancing Factor 2), AMAP2, centaurin beta-3, or PAG3. ASAP2 mediates the functions of Arf GTPases vial dual mechanisms: it exhibits GTPase activating protein (GAP) activity towards class I (Arf1) and II (Arf5) Arfs; and binds class III Arfs (GTP-Arf6) stably without GAP activity. It binds paxillin and is implicated in Fcgamma receptor-mediated phagocytosis in macrophages and in cell migration. ASAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, i
Probab=35.51  E-value=23  Score=13.42  Aligned_cols=68  Identities=16%  Similarity=0.323  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH-------CCHHHHHHHHHHHHH--HHHHHCCCCCCC
Q ss_conf             9999999987899998887999999899-9999999887530-------498999999999899--999840568833
Q gi|254780182|r  451 EVQTRAILELRLARLTGLGRDDIRNELN-SLGIEIKECLDIL-------SSRSRLLGIIKQELL--SVKDELDTPRRT  518 (910)
Q Consensus       451 e~QA~AILdMrL~rLt~LE~~kl~~E~~-eL~~~I~~l~~IL-------~s~~~l~~iI~~EL~--eik~kygd~RRT  518 (910)
                      -.|.+.|+..||.+|.+-+..+++.|++ ...+..++|+.-+       ....++.+++..|..  |+.+.+-.+||.
T Consensus        83 ~~n~~~~v~~pL~~f~k~DLk~~K~dlKK~FdKaskdyeak~~K~ek~k~~~aK~~g~~r~E~~~~E~a~~l~~eRr~  160 (215)
T cd07642          83 VQNMNNIITFPLDSLLKGDLKGVKGDLKKPFDKAWKDYETKVTKIEKEKKEHAKMHGMIRTEISGAEIAEEMEKERRF  160 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHCCCHHHHHHHHHHHHHH
T ss_conf             999999998799999998888736888726789889999999999888787433024511022167788999999999


No 145
>TIGR01341 aconitase_1 aconitate hydratase 1; InterPro: IPR006249   Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases.   Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA.    Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated .   IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.   Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.   This entry represents bacterial aconitase A (AcnA), eukaryotic cytosolic aconitase (cAcn/IRP1), iron regulatory protein 2 (IRP2), and a few mitochondrial aconitases (certain mAcn proteins, but not the majority of these enzymes).   More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0051539 4 iron 4 sulfur cluster binding, 0008152 metabolic process.
Probab=35.48  E-value=15  Score=14.93  Aligned_cols=74  Identities=20%  Similarity=0.260  Sum_probs=34.5

Q ss_pred             EEEEHHHCCCCCC---CCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCC-CCCCCCCEEEEE
Q ss_conf             5301788486675---774148876067777686899997289964999945998999990105544-515687388980
Q gi|254780182|r  810 KRTSSYDFRISNR---SGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIA-SRATKGVVIFST  885 (910)
Q Consensus       810 KRt~~~eyr~q~R---GgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~-gR~a~GV~i~~L  885 (910)
                      |-+=+.+|-.-+|   =|+||.=+.+...+..            +-  |-=++-.++.+++++|... -|..-=|+..+-
T Consensus       795 kaVIAeSFERIHRSNLVgMGviPl~f~~g~~a------------~T--LGl~G~E~~~id~~~i~~~~Pg~~vtv~~~~~  860 (896)
T TIGR01341       795 KAVIAESFERIHRSNLVGMGVIPLEFKQGEDA------------ET--LGLTGEELITIDVDDIKEIKPGKEVTVTLTNK  860 (896)
T ss_pred             EEEEECCCCHHHHHHHHHHCCCCCCCCCCCCC------------CC--CCCCCCEEEEEECCCCCCCCCCCCEEEEEECC
T ss_conf             79983253303323324304122105888871------------12--57875369998658866348897025899836


Q ss_pred             CCCCEEE--EEEEEC
Q ss_conf             8998799--999835
Q gi|254780182|r  886 AKDERVV--SVERIR  898 (910)
Q Consensus       886 ~~~D~Vv--~va~i~  898 (910)
                      + |++.+  .+.|+.
T Consensus       861 ~-G~~~t~~~~~R~D  874 (896)
T TIGR01341       861 D-GEKETFECVLRID  874 (896)
T ss_pred             C-CCEEEEEEEEEEC
T ss_conf             8-9788997888725


No 146
>TIGR03268 methan_mark_3 putative methanogenesis marker protein 3. A single member of this protein family is found in each of the first ten complete genome sequences of archaeal methanogens, and nowhere else. This protein family was detected by the method of partial phylogenetic profiling (see Haft, et al., 2006). The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis.
Probab=35.47  E-value=23  Score=13.41  Aligned_cols=170  Identities=16%  Similarity=0.163  Sum_probs=72.4

Q ss_pred             CCEEEEEEHHHCCC----CCCCCCCCEEEEECCC-CCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCC
Q ss_conf             98599975876235----4786655357675289-98699989733666542000001222333333345554--44444
Q gi|254780182|r  702 LGQCVRFPISAIRV----FAGRNSVGVRGISLAK-GDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDT--EEITS  774 (910)
Q Consensus       702 ~G~~lrF~~~evr~----~~GR~a~GVkgIkL~~-~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~  774 (910)
                      .|++-.+.++-...    .-||...|...+++.+ ||++ +....+.--.     ...+....+........+  .....
T Consensus       269 ~G~vYIYredr~ss~sHtvVG~V~~GiELid~a~~G~~l-tv~t~Peri~-----llGlt~~eA~~~~~~~gIe~~~dG~  342 (503)
T TIGR03268       269 EGRVYIYREDRPSSLSHNVVGHVTRGIELIDIAQEGDRL-SVETEPPRID-----LVGLTQEEAEELLEELGIELEKEGV  342 (503)
T ss_pred             CEEEEEECCCCCCCCCCCEEEEEECCEEEEEHHCCCCEE-EEEECCHHHE-----ECCCCHHHHHHHHHHCCCEEEECCC
T ss_conf             446999867878876630467880351321031479779-9984745704-----2388899999999866968984477


Q ss_pred             CCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEE--------HHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEE
Q ss_conf             443332222232001110125686799997599345301--------788486675774148876067777686899997
Q gi|254780182|r  775 LKNDSSVEGNISEERCQELKLKEQFILTVSEKGFGKRTS--------SYDFRISNRSGKGIRATDVSKINEIGALVAVFP  846 (910)
Q Consensus       775 ~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~--------~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~  846 (910)
                      ...++.+....+...+.-++...-.+..|.........-        +.=||.    ..|++.      .+.|.|---|.
T Consensus       343 ~~~daVVV~Q~P~~TleIL~~~kV~~~~v~~~~vi~IeLydd~AP~s~~yFR~----~tGL~~------~~VG~L~v~F~  412 (503)
T TIGR03268       343 DGDDAVVVKQEPPYTLDVLKEGKVKVEGVPKDKVIEIELYDDNAPRSVWYFRK----FTGLKT------KPVGRLPVHFA  412 (503)
T ss_pred             CCCCCEEEECCCCHHHHHHHCCCEEEEEECHHHEEEEEECCCCCCHHHHHHHH----HCCCCC------CCCCEEEEEEE
T ss_conf             78984899658942787752581799961868779999746578357899988----518752------43660577886


Q ss_pred             CCCCCEEEEE-ECCCEE----------EEEECCCCCCC--CCCCCCCEEEEECCCCE
Q ss_conf             2899649999-459989----------99990105544--51568738898089987
Q gi|254780182|r  847 VNDNDQIILV-SDKGTL----------IRVPVNEIRIA--SRATKGVVIFSTAKDER  890 (910)
Q Consensus       847 V~~~DeIlli-T~~G~i----------iR~~v~~I~~~--gR~a~GV~i~~L~~~D~  890 (910)
                      .++   ++|+ .+....          -++++..|-++  .|-..|.--++|.++|+
T Consensus       413 ~~d---~~lFk~~~~~~k~liPEN~P~~~V~ag~IgvTN~a~k~~G~iGVRl~d~de  466 (503)
T TIGR03268       413 FKE---MIMFKGNKELAKGLIPENTPEDKVEAGVIGVTNQACKHVGMIGVRLEDSDE  466 (503)
T ss_pred             ECC---EEEECCCCHHCCCCCCCCCCCCCCCCCEEEEECHHHHCCCEEEEEECCCCC
T ss_conf             387---799637811035568888887753234676660145418657898057754


No 147
>KOG3029 consensus
Probab=35.42  E-value=23  Score=13.41  Aligned_cols=45  Identities=16%  Similarity=0.390  Sum_probs=37.4

Q ss_pred             CCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCC
Q ss_conf             27321101676101013317898547899999988761877688888863458668
Q gi|254780182|r  170 RYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDF  225 (910)
Q Consensus       170 ~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDF  225 (910)
                      ++|.|++.|-.     |--+      .-||+++.-|+..|.-+++|+.++-|.-+|
T Consensus       136 KVPil~~~Geq-----m~dS------svIIs~laTyLq~~~q~l~eiiq~yPa~~~  180 (370)
T KOG3029         136 KVPILLIRGEQ-----MVDS------SVIISLLATYLQDKRQDLGEIIQMYPATSF  180 (370)
T ss_pred             CCCEEEECCCE-----ECHH------HHHHHHHHHHHCCCCCCHHHHHHHCCCCCC
T ss_conf             33079963614-----0205------899999999854678888999986664000


No 148
>TIGR01750 fabZ beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ; InterPro: IPR010084   Fatty acids biosynthesis occurs by two distinct pathways: in fungi, mammals and mycobacteria, type I or associative fatty-acid biosynthesis (type I FAS) is accomplished by multifunctional proteins in which distinct domains catalyse specific reactions; in plants and most bacteria, type II or dissociative fatty-acid biosynthesis (type II FAS) is accomplished by distinct enzymes .   FabZ is the primary dehydratase involved in fatty-acid elongation in type II FAS. Both FabZ and FabA catalyse the dehydration of beta-hydroxyacyl acyl carrier protein (ACP) to trans 2-enoyl ACP. However, FabZ and FabA display subtle differences in substrate specificities, whereby FabA is most effective on acyl ACPs of 9-11 carbon atoms in length, while FabZ is less specific. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains. ; GO: 0016836 hydro-lyase activity, 0006633 fatty acid biosynthetic process, 0005737 cytoplasm.
Probab=35.37  E-value=12  Score=15.84  Aligned_cols=28  Identities=29%  Similarity=0.487  Sum_probs=14.5

Q ss_pred             EEEECCC-CCCEEEEEEECCCCCCCCCCE
Q ss_conf             4545365-562002566301256668717
Q gi|254780182|r  620 NILSLNQ-GERITTIMPFPEDESSWNNLY  647 (910)
Q Consensus       620 nll~l~~-~E~I~ail~~~~~~~~~~~~~  647 (910)
                      ..++++. +.+|+|+=+++-.|-.-..||
T Consensus        21 Ri~e~~~~~~~ivA~KNVTINEPfF~GHF   49 (142)
T TIGR01750        21 RILELEPEGKRIVAIKNVTINEPFFQGHF   49 (142)
T ss_pred             EEEEEECCCCEEEEEEEEEECCCCCCCCC
T ss_conf             68887249978999711677489888988


No 149
>pfam08672 APC2 Anaphase promoting complex (APC) subunit 2. The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein.
Probab=35.35  E-value=23  Score=13.40  Aligned_cols=36  Identities=28%  Similarity=0.345  Sum_probs=22.9

Q ss_pred             EHHHHCCCCCCHHHHHHHHHHHHHCC---CCCHHHHHHH
Q ss_conf             01331789854789999998876187---7688888863
Q gi|254780182|r  184 VGMATNIPTHNLGEVVDGCVAVIDNP---DIDLDALMEI  219 (910)
Q Consensus       184 vGmaTnippHNl~Ev~~a~~~~i~~p---~~~~~eL~~~  219 (910)
                      |||-||.++-.|.-+..-+....-.|   ++|.++|-.|
T Consensus         3 ~gMLtN~~slpl~RIh~mLkmfv~~~~~~~~t~~eL~~f   41 (60)
T pfam08672         3 VGMLTNLGSLPLERIHSMLKMFPKDPGGYTISQEELEEF   41 (60)
T ss_pred             CHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHH
T ss_conf             208445787889999999997476999987699999999


No 150
>KOG0787 consensus
Probab=35.35  E-value=23  Score=13.40  Aligned_cols=44  Identities=14%  Similarity=0.166  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC-CCEE
Q ss_conf             9999999998875304989999999998999998405688-3310
Q gi|254780182|r  477 LNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPR-RTRI  520 (910)
Q Consensus       477 ~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~R-RT~I  520 (910)
                      .+.+.+--..+..|++.-.-..-.+.+-+.|.+++|+||- +..|
T Consensus       129 ~~~~~qf~d~l~~l~~rH~dvv~~lA~Gl~E~~~~~~dp~~~~~i  173 (414)
T KOG0787         129 LEDLSQFNDLLNTLRNRHNDVVPTLAQGLIEYREKDGDPVTEKNI  173 (414)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             330999999999997302105899998899999852884067789


No 151
>pfam11892 DUF3412 Domain of unknown function (DUF3412). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain is found associated with pfam03641.
Probab=35.27  E-value=22  Score=13.61  Aligned_cols=57  Identities=16%  Similarity=0.458  Sum_probs=37.9

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCCCEEE---------EHHHHHHH----------HCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf             00089736789999999878999998113---------40425566----------436688704789999997122011
Q gi|254780182|r   45 LRDGLKPVHRRILFGMMQMGVEWNKKYVK---------CARISGEV----------MGKYHPHGNAAIYDALARMAQDWS  105 (910)
Q Consensus        45 ~rDGlKpv~Rrily~m~~~~~~~~~~~~K---------~a~ivg~v----------~gkyHPHGd~siy~a~v~maq~~~  105 (910)
                      ..--+-|.|-    .|..|.|+.+.|--.         |.=|.|.|          -|-|.-|||..|.++|=.+-|.|.
T Consensus        28 fQ~PF~PTHe----nMa~L~L~~~qp~~~LAanLRrAFSGIVAGNVK~~gi~~Ie~~GPf~i~GD~~im~~lD~LL~~FV  103 (123)
T pfam11892        28 FQQPFEPTHE----NMANLNLHRDQPPHELAANLRRAFSGIVAGNVKEEGIRAIEKHGPFEIHGDPELMKKMDKLLQAFV  103 (123)
T ss_pred             HCCCCCCCHH----HHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHH
T ss_conf             6489888477----786464787799899999999986364205546799999997699155088999999999999999


No 152
>TIGR03449 mycothiol_MshA UDP-N-acetylglucosamine: 1L-myo-inositol-1-phosphate 1-alpha-D-N-acetylglucosaminyltransferase. Members of this protein family, found exclusively in the Actinobacteria, are MshA, the glycosyltransferase of mycothiol biosynthesis. Mycothiol replaces glutathione in these species.
Probab=35.20  E-value=23  Score=13.38  Aligned_cols=18  Identities=11%  Similarity=0.257  Sum_probs=9.2

Q ss_pred             CCCCCHHHHHHHHHHHHH
Q ss_conf             898547899999988761
Q gi|254780182|r  190 IPTHNLGEVVDGCVAVID  207 (910)
Q Consensus       190 ippHNl~Ev~~a~~~~i~  207 (910)
                      .|-.|+..+++|+-.+++
T Consensus       229 ~~~Kg~~~li~A~~~l~~  246 (405)
T TIGR03449       229 QPLKAPDVLLRAVAELLD  246 (405)
T ss_pred             CHHHHHHHHHHHHHHHHH
T ss_conf             501148999999999998


No 153
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol 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.  There are two major groups of dioxygenases 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 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, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=34.90  E-value=23  Score=13.34  Aligned_cols=26  Identities=23%  Similarity=0.225  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             23699999999987899998887999
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRDD  472 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~k  472 (910)
                      |+||+.|-+||++--...|..+..+-
T Consensus        33 ~~Lt~ee~~al~~~D~~~L~~lGvn~   58 (77)
T cd07321          33 YGLTPEEKAALLARDVGALYVLGVNP   58 (77)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHCCCCH
T ss_conf             69999999998856899999979969


No 154
>PRK09458 pspB phage shock protein B; Provisional
Probab=34.83  E-value=23  Score=13.34  Aligned_cols=25  Identities=12%  Similarity=0.205  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             9999989999999998875304989
Q gi|254780182|r  471 DDIRNELNSLGIEIKECLDILSSRS  495 (910)
Q Consensus       471 ~kl~~E~~eL~~~I~~l~~IL~s~~  495 (910)
                      +.|-+..+.+.++|..|+.||+.+.
T Consensus        45 ~~L~~~A~~m~eRI~tLE~ILDae~   69 (75)
T PRK09458         45 AQLTEKAEKMRERIQTLEAILDAEH   69 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9999999999999999999972669


No 155
>KOG4649 consensus
Probab=34.79  E-value=23  Score=13.33  Aligned_cols=28  Identities=11%  Similarity=0.075  Sum_probs=21.1

Q ss_pred             CEEEEEECCCCEEEEEHHH---CCCCCCCCC
Q ss_conf             6799997599345301788---486675774
Q gi|254780182|r  798 QFILTVSEKGFGKRTSSYD---FRISNRSGK  825 (910)
Q Consensus       798 ~~IL~vTe~G~GKRt~~~e---yr~q~RGgk  825 (910)
                      .+++..++-|---+..+++   |...+-++.
T Consensus       250 ghL~w~~~~g~t~~vy~~p~l~F~~h~~~~S  280 (354)
T KOG4649         250 GHLLWATQSGTTLHVYLSPKLRFDLHSPGIS  280 (354)
T ss_pred             CEEEEEECCCCEEEEEECCCCCEECCCCCCC
T ss_conf             4189983477089999576421003687886


No 156
>TIGR01090 apt adenine phosphoribosyltransferase; InterPro: IPR005764    Adenine phosphoribosyltransferase (APRTase, 2.4.2.7 from EC) is a widely distributed enzyme, and its deficiency in humans causes the accumulation of 2,8-dihydroxyadenine. It is the sole catalyst for adenine recycling in most eukaryotes.  AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate  ; GO: 0003999 adenine phosphoribosyltransferase activity, 0006168 adenine salvage.
Probab=34.23  E-value=15  Score=15.09  Aligned_cols=51  Identities=27%  Similarity=0.393  Sum_probs=32.4

Q ss_pred             CCCHHHHHHHHHHHHHCCC--CCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEE
Q ss_conf             8547899999988761877--68888886345866887443447588999987012038999
Q gi|254780182|r  192 THNLGEVVDGCVAVIDNPD--IDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIR  251 (910)
Q Consensus       192 pHNl~Ev~~a~~~~i~~p~--~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR  251 (910)
                      |--++.++|.++..+++-+  ++.|    +|=|||=  =|.|.|   -.=||++|-|=|-||
T Consensus        28 ~~~f~~~id~l~~~~~~~~~~id~d----~iVG~Ea--RGFifG---~~LA~~LgvGFVPVR   80 (175)
T TIGR01090        28 PELFRFLIDLLVERYKDANGEIDAD----LIVGLEA--RGFIFG---AALAYKLGVGFVPVR   80 (175)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCEE----EEECCCC--CHHHHH---HHHHHHHCCCEEEEE
T ss_conf             7789999999999998607951513----6876766--725778---899997089806754


No 157
>PTZ00233 variable surface protein Vir18; Provisional
Probab=34.22  E-value=18  Score=14.31  Aligned_cols=39  Identities=13%  Similarity=0.080  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHH-----HCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999999988753-----0498999999999899999840568
Q gi|254780182|r  477 LNSLGIEIKECLDI-----LSSRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       477 ~~eL~~~I~~l~~I-----L~s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      ..|..++|..|.++     -..=..|++.|++-=.|||.=|...
T Consensus        31 K~eIEqkId~f~~~~~~nfyk~w~~L~k~I~~KN~ElK~Cy~~~   74 (509)
T PTZ00233         31 KSDIEQKIDDFNKATHTNIYTQWDQLNKYIITKDAELKHCYDNG   74 (509)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999998612630367889999999876025776653078


No 158
>KOG0596 consensus
Probab=34.22  E-value=24  Score=13.26  Aligned_cols=10  Identities=20%  Similarity=0.770  Sum_probs=3.9

Q ss_pred             HCCCCCCCCC
Q ss_conf             3458668874
Q gi|254780182|r  219 IIRGPDFPTG  228 (910)
Q Consensus       219 ~i~GPDFPTG  228 (910)
                      ++.+||.||-
T Consensus       215 ~~~k~nlp~~  224 (677)
T KOG0596         215 LLNKPNLPVK  224 (677)
T ss_pred             CCCCCCCCCC
T ss_conf             0258998866


No 159
>PTZ00156 60S ribosomal protein L11; Provisional
Probab=33.82  E-value=24  Score=13.21  Aligned_cols=61  Identities=26%  Similarity=0.464  Sum_probs=27.0

Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCHHCCCCCCCCCCCCC
Q ss_conf             0897367899999998789999981134042556643668870478999999712--20111561314788708
Q gi|254780182|r   47 DGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMA--QDWSLRLLLIEGQGNFG  118 (910)
Q Consensus        47 DGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~ma--q~~~~r~plidg~GnfG  118 (910)
                      -|-|||.++-=++....|+..+-|-  .++|   ++     .|+.+ |+-|-|+-  .+|..+--=.|.+|||+
T Consensus        40 TGQkPv~tkAkkti~~F~iRkg~pI--G~kV---TL-----Rg~ka-~efL~r~l~v~d~~L~~~~Fd~~GNfs  102 (172)
T PTZ00156         40 TGQKPVFSKARLTVRSFGIRRNEKI--AVHC---TV-----RGKKA-EEILERGLKVKEFELKKRNFSDTGNFG  102 (172)
T ss_pred             HCCCCEEEEECCCHHCCCCCCCCEE--EEEE---EE-----CHHHH-HHHHHHHHHHCCCCCCCCCCCCCCCEE
T ss_conf             3997136531100110476789857--8999---97-----66889-999999884314673623528998514


No 160
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=33.75  E-value=24  Score=13.20  Aligned_cols=35  Identities=11%  Similarity=0.195  Sum_probs=24.2

Q ss_pred             HHHHHHHHHCCCCCCCCCCH-HHHHHHHHHHHCCCCCC
Q ss_conf             77998863137540008973-67899999998789999
Q gi|254780182|r   32 YAINVILGRAIPDLRDGLKP-VHRRILFGMMQMGVEWN   68 (910)
Q Consensus        32 Ya~svI~~RAlPd~rDGlKp-v~Rrily~m~~~~~~~~   68 (910)
                      .+.+ -++|||-+- ++.+| ...||+-++.+||..||
T Consensus        11 VS~~-TVSr~ln~~-~~vs~~tr~rI~~~a~~lgY~pN   46 (46)
T pfam00356        11 VSKA-TVSRVLNNP-ERVSEETREKVEAAMEELGYVPN   46 (46)
T ss_pred             CCHH-HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             7999-999998797-98999999999999999789999


No 161
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=33.75  E-value=24  Score=13.20  Aligned_cols=45  Identities=7%  Similarity=0.227  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHCCC
Q ss_conf             999999899999999988753049--899999999989999984056
Q gi|254780182|r  470 RDDIRNELNSLGIEIKECLDILSS--RSRLLGIIKQELLSVKDELDT  514 (910)
Q Consensus       470 ~~kl~~E~~eL~~~I~~l~~IL~s--~~~l~~iI~~EL~eik~kygd  514 (910)
                      ......||+.+.+.+++.+.+|++  +..+.....+|+.+++++...
T Consensus        48 iv~~~~~~~~~~~~l~~a~~~l~~~~D~em~ema~~Ei~~~~~~~~~   94 (363)
T COG0216          48 IVEKYREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIKELEAKIEE   94 (363)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999983568878999999999999998999


No 162
>PRK12806 flagellin; Provisional
Probab=33.61  E-value=24  Score=13.18  Aligned_cols=62  Identities=21%  Similarity=0.380  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             89999998740699999986189978987877631269788999997402211122234452369999999998789999
Q gi|254780182|r  386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL  465 (910)
Q Consensus       386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL  465 (910)
                      -+.||-.|..|.-.-|.++.-++      ..|-+                                .  ..||. |+|.|
T Consensus        57 qi~gl~qa~~N~~dgiSl~qtAe------gAL~e--------------------------------v--~~iLq-RmReL   95 (475)
T PRK12806         57 QIRGMNQAVRNANDGISLAQVAE------GAMQE--------------------------------T--TNILQ-RMREL   95 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH------HHHHH--------------------------------H--HHHHH-HHHHH
T ss_conf             99889999998998999999999------99999--------------------------------9--99999-99999


Q ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------88879999998999999999887
Q gi|254780182|r  466 ---------TGLGRDDIRNELNSLGIEIKECL  488 (910)
Q Consensus       466 ---------t~LE~~kl~~E~~eL~~~I~~l~  488 (910)
                               +.-++..|++|+++|..+|..+-
T Consensus        96 AvQAaNgTn~~~DR~aiq~Ei~qL~~eIdrIa  127 (475)
T PRK12806         96 SVQAANSTNNSSDRASIQSEISQLKSELERIA  127 (475)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99861688877889999999999999998786


No 163
>KOG1302 consensus
Probab=33.42  E-value=24  Score=13.16  Aligned_cols=16  Identities=38%  Similarity=0.702  Sum_probs=8.6

Q ss_pred             CCCCHHHHHHHHHHHH
Q ss_conf             0897367899999998
Q gi|254780182|r   47 DGLKPVHRRILFGMMQ   62 (910)
Q Consensus        47 DGlKpv~Rrily~m~~   62 (910)
                      -|++++-||-|...-+
T Consensus        15 ~~lq~~a~~eL~~lLd   30 (600)
T KOG1302          15 QGLQEVARRELISLLD   30 (600)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             8879999999999996


No 164
>cd00225 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin.
Probab=33.31  E-value=24  Score=13.15  Aligned_cols=41  Identities=17%  Similarity=0.172  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             78999988879999998999999999887530498999999
Q gi|254780182|r  460 LRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGI  500 (910)
Q Consensus       460 MrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~i  500 (910)
                      .+||.||.-|..+|.+-.++..+-.++++.+|+-+.+-|+.
T Consensus        26 ~~lReLt~~Eq~Ela~y~~e~~~yK~~~k~~l~er~~~~~~   66 (159)
T cd00225          26 FPLRELTPDEQQELAQYVEDVADYKEEVKQALKERQEGLKL   66 (159)
T ss_pred             CCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             22221888899999999999999999999999999988887


No 165
>TIGR02171 Fb_sc_TIGR02171 Fibrobacter succinogenes paralogous family TIGR02171.
Probab=33.30  E-value=24  Score=13.14  Aligned_cols=166  Identities=19%  Similarity=0.196  Sum_probs=79.4

Q ss_pred             HHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEE
Q ss_conf             98999998405688331001343453010145678189990797052331000002334565211000146410101133
Q gi|254780182|r  503 QELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFI  582 (910)
Q Consensus       503 ~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~  582 (910)
                      +=|+=+-+-||+=++|.+..-.+..+...|  .+.|    =+.|=-+.- +.+-..-.||-.-...++++ .|+|=+=++
T Consensus       222 N~lEwVNDW~~~F~dtTltNyvGs~d~~~l--g~~V----VKGGsY~~~-ps~~~ly~RGDVYPv~~St~-~DY~GFRLv  293 (982)
T TIGR02171       222 NVLEWVNDWYASFKDTTLTNYVGSSDEGSL--GERV----VKGGSYRNS-PSAINLYTRGDVYPVTSSTK-GDYVGFRLV  293 (982)
T ss_pred             CHHHHHCCCCCCCCCCCEEEEECCCCCCCC--CCCE----EECCCCCCC-CCCEECCCCCCCCCEECCCC-CCCCEEEEE
T ss_conf             122200560003125620103056775443--6634----535754567-23200147886312003787-762034441


Q ss_pred             ECCCCEEEEEECCCCEEEEECCCCC--CCCCCCCCC--CCEE------------EEECCCCC-CEEEEE----EECCCCC
Q ss_conf             2377739999548939998200043--224445655--4124------------54536556-200256----6301256
Q gi|254780182|r  583 VSTHTSVLFFSSLGFVYKEKVWRLP--IGSPQARGK--ALIN------------ILSLNQGE-RITTIM----PFPEDES  641 (910)
Q Consensus       583 ~~t~d~LLfFTs~Gkvy~l~v~~IP--~~sr~skG~--pi~n------------ll~l~~~E-~I~ail----~~~~~~~  641 (910)
                      |=+-+.=+-|+++|.+-.-++.-+=  ..=|.--|+  .=..            |++...+- +|+-|.    .++.+- 
T Consensus       294 ~G~IPdA~wLd~~G~v~t~~~~~~~~~~~~r~~~gtkky~~KLaFRND~TgnL~yIDy~~~~~~~~EI~D~~~vyHPDI-  372 (982)
T TIGR02171       294 LGAIPDATWLDESGKVATSKVKSLISSSEIRELTGTKKYKAKLAFRNDVTGNLAYIDYAKGASKVVEIEDTIKVYHPDI-  372 (982)
T ss_pred             CCCCCCCCCCCCCCCEEEEEEEEEEEHHHHHHHHCCEEEEEEEEEECCCCCCEEEEEECCCCCEEEEEECCCCEECCCC-
T ss_conf             1488875541888967688878752058888530770367777870476433268870588336998303741202740-


Q ss_pred             CCCCCEEEEEEC-CCCEEEECHHHHH-HCCCCCEEEEEEC
Q ss_conf             668717999947-9918984236862-0477722786615
Q gi|254780182|r  642 SWNNLYVVFATK-HGNVRRNKLSDFI-QINRSGKIAMKLD  679 (910)
Q Consensus       642 ~~~~~~Lvl~Tk-~G~VKkt~l~ef~-~~r~~G~~aikLk  679 (910)
                      ..+..++-|||. -|.-++.++  |. ++..+|--..||.
T Consensus       373 SPDG~~VAFCT~~EG~~GkS~v--YVR~Ln~~G~~LVKL~  410 (982)
T TIGR02171       373 SPDGKKVAFCTGIEGVDGKSEV--YVRDLNASGSGLVKLD  410 (982)
T ss_pred             CCCCCEEEEECCCCCCCCCCEE--EEECCCCCCCCCEEEC
T ss_conf             7986874576341144787438--9844555789812206


No 166
>TIGR03300 assembly_YfgL outer membrane assembly lipoprotein YfgL. Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ.
Probab=33.05  E-value=25  Score=13.11  Aligned_cols=59  Identities=10%  Similarity=-0.071  Sum_probs=28.6

Q ss_pred             CCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEEC
Q ss_conf             678189990797052331000002334565211000146410101133237773999954893999820
Q gi|254780182|r  535 REDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKV  603 (910)
Q Consensus       535 ~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v  603 (910)
                      ..+.+.+.+.+|.|..+...+=+..=         +.+-++.+. .-.+-..+.+++-|..|.+|.+.+
T Consensus        64 ~~~~vy~~~~~G~v~Ald~~tG~~~W---------~~~~~~~i~-~g~~v~~~~v~vgt~~G~l~Ald~  122 (377)
T TIGR03300        64 AGGKVYAADADGTVVALDAETGKRLW---------RVDLDERLS-GGVGADGGLVFVGTEKGEVIALDA  122 (377)
T ss_pred             ECCEEEEECCCCEEEEEECCCCCEEE---------EEECCCCEE-EEEEEECCEEEEEECCCEEEEEEC
T ss_conf             89999998499759999965894887---------888699815-603882999999909975999997


No 167
>COG0493 GltD NADPH-dependent glutamate synthase beta chain and related oxidoreductases [Amino acid transport and metabolism / General function prediction only]
Probab=33.02  E-value=19  Score=14.07  Aligned_cols=130  Identities=23%  Similarity=0.284  Sum_probs=60.6

Q ss_pred             HCCCC--CCCCCC---CCC-CHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             34586--688744---344-758899998701203899998865433678459999246443528999999999987166
Q gi|254780182|r  219 IIRGP--DFPTGA---VIL-GRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKR  292 (910)
Q Consensus       219 ~i~GP--DFPTGG---~I~-~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~k  292 (910)
                      ++|++  -=+||-   +|- |..|+..++.--+=...|-. ++-+...+|   ++-+-||=    -++-..|        
T Consensus       112 ~i~~~~~~~~tg~~VaviGaGPAGl~~a~~L~~~G~~Vtv-~e~~~~~GG---ll~yGIP~----~kl~k~i--------  175 (457)
T COG0493         112 WIPGELPGSRTGKKVAVIGAGPAGLAAADDLSRAGHDVTV-FERVALDGG---LLLYGIPD----FKLPKDI--------  175 (457)
T ss_pred             CCCCCCCCCCCCCEEEEECCCCHHHHCHHHHHHCCCEEEE-CCCCCCCCE---EEEECCCH----HHCCCHH--------
T ss_conf             9788788887676799988895155588999868987998-266677744---79814844----6464206--------


Q ss_pred             CCHHHHHHHHC-CCCCEEEEEEECC--CCCHHHHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             50144587303-7465579999479--88778999999976101100000024554166300029999999999999999
Q gi|254780182|r  293 IVDIADLRDES-DRQGYRVVIELKR--GASADVILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVV  369 (910)
Q Consensus       293 i~gI~dirDeS-dr~giRivielKr--~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi  369 (910)
                          .|-+=++ -+.|+.+++-.++  ++..+.++..          |-.-+++.-.++|+.+++...=..-+.+..+-+
T Consensus       176 ----~d~~i~~l~~~Gv~~~~~~~vG~~it~~~L~~e----------~Dav~l~~G~~~~~~l~i~g~d~~gv~~A~dfL  241 (457)
T COG0493         176 ----LDRRLELLERSGVEFKLNVRVGRDITLEELLKE----------YDAVFLATGAGKPRPLDIPGEDAKGVAFALDFL  241 (457)
T ss_pred             ----HHHHHHHHHHCCCEEEECCEECCCCCHHHHHHH----------HCEEEEECCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             ----899999998749099986677996789998653----------287999326678876898886777761687999


Q ss_pred             HHHHHHHHH
Q ss_conf             999999999
Q gi|254780182|r  370 VRRTKYLLN  378 (910)
Q Consensus       370 ~rRt~~~L~  378 (910)
                      ++-++..|.
T Consensus       242 ~~~~~~~~~  250 (457)
T COG0493         242 TRLNKEVLG  250 (457)
T ss_pred             HHHHHHHCC
T ss_conf             999998603


No 168
>pfam07569 Hira TUP1-like enhancer of split. The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain pfam00400.
Probab=32.91  E-value=25  Score=13.10  Aligned_cols=27  Identities=19%  Similarity=0.511  Sum_probs=20.2

Q ss_pred             EEEEECCCCEEEEEECCCCEEEEECCCCCCC
Q ss_conf             1133237773999954893999820004322
Q gi|254780182|r  579 DLFIVSTHTSVLFFSSLGFVYKEKVWRLPIG  609 (910)
Q Consensus       579 ~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~  609 (910)
                      .++.|+. .+|+++|+.|-+|.   |++...
T Consensus        16 ~~Le~~~-~~Ll~iT~~G~l~v---Wnv~~~   42 (219)
T pfam07569        16 SFLESNG-SYLLCVTSVGLLYV---WNVKTK   42 (219)
T ss_pred             EEEEECC-CEEEEEECCCEEEE---EECCCC
T ss_conf             6998179-78999925887999---976598


No 169
>KOG3091 consensus
Probab=32.89  E-value=25  Score=13.09  Aligned_cols=95  Identities=17%  Similarity=0.188  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHH
Q ss_conf             99999998887789999998740699999986189978987877631269788999997402211122234452369999
Q gi|254780182|r  374 KYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQ  453 (910)
Q Consensus       374 ~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~Q  453 (910)
                      .-+|+...+++.-|.     -...|.+++|       ++||.++++-                             |.+ 
T Consensus       354 r~ri~~i~e~v~eLq-----k~~ad~~~KI-------~~~k~r~~~L-----------------------------s~R-  391 (508)
T KOG3091         354 RIRINAIGERVTELQ-----KHHADAVAKI-------EEAKNRHVEL-----------------------------SHR-  391 (508)
T ss_pred             HHHHHHHHHHHHHHH-----HHHHHHHHHH-------HHHHHHHHHH-----------------------------HHH-
T ss_conf             999999998999987-----6301578899-------9999877779-----------------------------999-


Q ss_pred             HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             999998789999888799-----99998999999999887530498999999999899999840568833
Q gi|254780182|r  454 TRAILELRLARLTGLGRD-----DIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRT  518 (910)
Q Consensus       454 A~AILdMrL~rLt~LE~~-----kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT  518 (910)
                             -||=++++|..     -|..+.++|+++...|..-|+.+.++|..+ .+|.++.+--.+.++.
T Consensus       392 -------iLRv~ikqeilr~~G~~L~~~EE~Lr~Kldtll~~ln~Pnq~k~Rl-~~L~e~~r~q~~~~~~  453 (508)
T KOG3091         392 -------ILRVMIKQEILRKRGYALTPDEEELRAKLDTLLAQLNAPNQLKARL-DELYEILRMQNSQLKL  453 (508)
T ss_pred             -------HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHH-HHHHHHHHHHCCHHCC
T ss_conf             -------9999999999860487689658999999999998752829899999-9999999754001204


No 170
>cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=32.60  E-value=25  Score=13.06  Aligned_cols=30  Identities=7%  Similarity=0.127  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999878999988879999998999999
Q gi|254780182|r  453 QTRAILELRLARLTGLGRDDIRNELNSLGI  482 (910)
Q Consensus       453 QA~AILdMrL~rLt~LE~~kl~~E~~eL~~  482 (910)
                      |++.++--||.++.+-+....++..+...+
T Consensus        83 q~~~~v~~pL~~f~k~dl~~vKe~KK~FdK  112 (200)
T cd07603          83 QAQRTVSTQLQNFVKEDIKKVKESKKHFEK  112 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999736899998889998


No 171
>PRK07004 replicative DNA helicase; Provisional
Probab=32.38  E-value=25  Score=13.03  Aligned_cols=23  Identities=35%  Similarity=0.521  Sum_probs=12.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98999999999899999840568
Q gi|254780182|r  493 SRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       493 s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      ++......|-..|+.+.+.++-|
T Consensus       344 ~r~~ei~~isr~lK~lAkel~ip  366 (460)
T PRK07004        344 NRATEISEISRSLKSLAKELDVP  366 (460)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             89999999999999999996997


No 172
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which  play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=32.16  E-value=25  Score=13.00  Aligned_cols=25  Identities=28%  Similarity=0.420  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      |+||+.|-+||++....+|-.+.-+
T Consensus        51 ~~Lteeqk~aV~~RD~~~li~lGgn   75 (121)
T cd07924          51 WPMTEEQKQAVLARDYNRMLALGGN   75 (121)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             6999999999997479999992682


No 173
>KOG3957 consensus
Probab=32.12  E-value=23  Score=13.44  Aligned_cols=27  Identities=26%  Similarity=0.578  Sum_probs=19.9

Q ss_pred             CCCCCCCCCC--C-HHHHHHHHHHCCCEEE
Q ss_conf             6688744344--7-5889999870120389
Q gi|254780182|r  223 PDFPTGAVIL--G-RTGIKNAYATGRGSIV  249 (910)
Q Consensus       223 PDFPTGG~I~--~-~~~i~~~y~tGrG~i~  249 (910)
                      -||.|||.--  + -.+|.+-|+||||-+.
T Consensus       152 aDfAgGgL~aa~gI~~AL~~RtrtgkGqvi  181 (387)
T KOG3957         152 ADFAGGGLYAAGGILAALYQRTRTGKGQVI  181 (387)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHCCCCCEEE
T ss_conf             442365068999999999998416885488


No 174
>PHA02126 hypothetical protein
Probab=31.90  E-value=23  Score=13.45  Aligned_cols=50  Identities=26%  Similarity=0.302  Sum_probs=32.3

Q ss_pred             CCCCCCCCC-CHHHHHHHHHHCCCEEE-------EEEEEEEEECCCCCEEEEEECCCC
Q ss_conf             688744344-75889999870120389-------999886543367845999924644
Q gi|254780182|r  224 DFPTGAVIL-GRTGIKNAYATGRGSIV-------IRGVSHIEKTSGDREQIVVTEIPY  273 (910)
Q Consensus       224 DFPTGG~I~-~~~~i~~~y~tGrG~i~-------iR~k~~ie~~~~~k~~ivItEiPY  273 (910)
                      -.|.|+.|+ +++-|.++-.-|..+-+       -|-|.|+|-+.+----|.+||+|.
T Consensus        50 qlpggalivadrd~i~~~r~~~~nk~rmldtlsfcrdkmhfell~rppviif~t~~~~  107 (153)
T PHA02126         50 QLPGGALIVADRDIITSIRRAGGNKPRMLDTLSFCRDKMHFELLGRPPVIIFNTQTPL  107 (153)
T ss_pred             CCCCCEEEEECHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCH
T ss_conf             4898438995478899886236897425677887654466876189988999536756


No 175
>TIGR01052 top6b DNA topoisomerase VI, B subunit; InterPro: IPR005734   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea, but also in a few eukayotes, such as the plant  Arabidopsis thaliana . This enzyme assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein that mediates double-strand DNA breaks during meiotic recombination in eukaryotes . Therefore, though related to type IIA topoisomerases, topoisomerase VI may have a distinctive mechanism of action.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=31.63  E-value=22  Score=13.55  Aligned_cols=15  Identities=27%  Similarity=0.428  Sum_probs=7.9

Q ss_pred             CCCCCEEEEEEECCC
Q ss_conf             374655799994798
Q gi|254780182|r  303 SDRQGYRVVIELKRG  317 (910)
Q Consensus       303 Sdr~giRivielKr~  317 (910)
                      +...|+||.+|+|-+
T Consensus       172 ~~W~GTriEle~~~v  186 (662)
T TIGR01052       172 GSWRGTRIELEVKDV  186 (662)
T ss_pred             CCCEEEEEEEEEECC
T ss_conf             981368999998222


No 176
>cd04637 CBS_pair_24 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=31.45  E-value=26  Score=12.91  Aligned_cols=41  Identities=15%  Similarity=0.305  Sum_probs=20.4

Q ss_pred             HHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHCCCCCCCCCCCC
Q ss_conf             425566436688---704789999997122011156131478870
Q gi|254780182|r   76 RISGEVMGKYHP---HGNAAIYDALARMAQDWSLRLLLIEGQGNF  117 (910)
Q Consensus        76 ~ivg~v~gkyHP---HGd~siy~a~v~maq~~~~r~plidg~Gnf  117 (910)
                      +-|+++|-+ +|   +.++.+++|+-.|.+.---+.|.+|.+|..
T Consensus        67 ~~v~~iM~~-~~itv~~~~~l~~a~~~m~~~~i~~lPVvd~~~~l  110 (122)
T cd04637          67 RRAHQIMTR-DPITVSPDTPVDEASKLLLENSISCLPVVDENGQL  110 (122)
T ss_pred             CCHHHHCCC-CCEEECCCCCHHHHHHHHHHCCCEEEEEECCCCEE
T ss_conf             899994638-98399999849999999997493089999689989


No 177
>pfam02624 YcaO YcaO-like family.
Probab=31.45  E-value=22  Score=13.48  Aligned_cols=78  Identities=21%  Similarity=0.312  Sum_probs=41.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCC-CCCCCCEECCCCCCCCCEECCCCCCCCHH-----------CCCCCEEEHHHHCC
Q ss_conf             9720135789997899999986307-68405330689885485034322732110-----------16761010133178
Q gi|254780182|r  123 DPPAAERYTECRLQKAAHFLLDDLG-KDTVDFRPNYDGSFQEPVVLCARYPNVLV-----------NGGGGIAVGMATNI  190 (910)
Q Consensus       123 d~~AA~RYte~rl~~~~~~~l~~i~-~~tv~~~~n~D~~~~EP~vlP~~~P~lL~-----------nG~~GIAvGmaTni  190 (910)
                      ||..-.+|.........  .....+ ...+.|++-+|=...+|+.+|+.+=.+-.           -.|+|.|.|-... 
T Consensus        47 ~p~~~~~~~~~q~~~~~--~~~~~~~d~~i~Wv~~~~l~~g~~v~vP~~~v~~~~~~~~~~~~~~~~~SnGlAaG~t~~-  123 (332)
T pfam02624        47 DPEDLVLYSDEQYAKPG--FPNPYDPDLPLEWVPGWDLLSGEEVYVPANLVYVSNPYPGGEDRFFPSTSNGLAAGNTLE-  123 (332)
T ss_pred             CHHHHCCCCHHHHCCCC--CCCCCCCCCEEEEEEEEECCCCCEEEEEHHHHHCCCCCCCCCCCEECCCCCEECCCCCHH-
T ss_conf             99997268766641335--677789898051068588489968997379973478888766732124787236889999-


Q ss_pred             CCCCHHHHHHHHHHHHHC
Q ss_conf             985478999999887618
Q gi|254780182|r  191 PTHNLGEVVDGCVAVIDN  208 (910)
Q Consensus       191 ppHNl~Ev~~a~~~~i~~  208 (910)
                           .=++.|+.-+|+.
T Consensus       124 -----eA~~~gl~EvIER  136 (332)
T pfam02624       124 -----EAILHGLLEVIER  136 (332)
T ss_pred             -----HHHHHHHHHHHHH
T ss_conf             -----9999999999999


No 178
>cd04605 CBS_pair_MET2_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the MET2 domain. Met2 is a key enzyme in the biosynthesis of methionine.  It encodes a homoserine transacetylase involved in converting homoserine to O-acetyl homoserine. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=31.44  E-value=24  Score=13.15  Aligned_cols=27  Identities=22%  Similarity=0.311  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHCCCHHCCCCCCCCCCCC
Q ss_conf             789999997122011156131478870
Q gi|254780182|r   91 AAIYDALARMAQDWSLRLLLIEGQGNF  117 (910)
Q Consensus        91 ~siy~a~v~maq~~~~r~plidg~Gnf  117 (910)
                      +++++|+-.|.+.-....|.+|.+|.+
T Consensus        11 ~tv~~a~~~m~~~~~~~lpVvd~~~~~   37 (110)
T cd04605          11 ASIKEAAKLMIEENINHLPVVDEDGRL   37 (110)
T ss_pred             CCHHHHHHHHHHCCCCEEEEECCCCCE
T ss_conf             999999999997299889999799919


No 179
>KOG0319 consensus
Probab=31.42  E-value=26  Score=12.91  Aligned_cols=183  Identities=12%  Similarity=0.133  Sum_probs=90.4

Q ss_pred             CCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCC
Q ss_conf             01456781899907970523310000023345652110001464101011332377739999548939998200043224
Q gi|254780182|r  531 DCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGS  610 (910)
Q Consensus       531 dlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~s  610 (910)
                      =+=|+|..+.+-|+.+-+|-.....-..|--         ---.|.|..+-+..+.   .+|-+-+|=-+...|.+-...
T Consensus       331 ~lG~e~~~laVATNs~~lr~y~~~~~~c~ii---------~GH~e~vlSL~~~~~g---~llat~sKD~svilWr~~~~~  398 (775)
T KOG0319         331 FLGPEESHLAVATNSPELRLYTLPTSYCQII---------PGHTEAVLSLDVWSSG---DLLATGSKDKSVILWRLNNNC  398 (775)
T ss_pred             ECCCCCCEEEEEECCCCEEEEECCCCCEEEE---------ECCHHHEEEEEECCCC---CEEEEECCCCEEEEEEECCCC
T ss_conf             1177545599970797169896499753787---------0754550454321367---389983588669999945896


Q ss_pred             CCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEE----CCCCEEEE
Q ss_conf             44565541245453655620025663012566687179999479918984236862047772278661----58985788
Q gi|254780182|r  611 PQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKL----DSRDEILS  686 (910)
Q Consensus       611 r~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikL----kegD~Li~  686 (910)
                        ++-.++...-..  .-.|.+ +...    .....|++.++.++.+|...+.. +..... -+.++.    .--|+=|.
T Consensus       399 --~~~~~~a~~~gH--~~svga-va~~----~~~asffvsvS~D~tlK~W~l~~-s~~~~~-~~~~~~~~t~~aHdKdIN  467 (775)
T KOG0319         399 --SKSLCVAQANGH--TNSVGA-VAGS----KLGASFFVSVSQDCTLKLWDLPK-SKETAF-PIVLTCRYTERAHDKDIN  467 (775)
T ss_pred             --CHHHHHHHHCCC--CCCCCE-EEEC----CCCCCEEEEECCCCEEEEECCCC-CCCCCC-CCEEHHHHHHHHHCCCCC
T ss_conf             --055436664266--654212-5641----46753899914870699853788-634356-603125677786456565


Q ss_pred             EEECCCCCEEE-EEEC--CCEEEEEEHHHCC---CCCCCCCCCEEEEECCCCCEEEEEE
Q ss_conf             89618982699-9936--9859997587623---5478665535767528998699989
Q gi|254780182|r  687 VETCTQENDIL-LTTK--LGQCVRFPISAIR---VFAGRNSVGVRGISLAKGDQVISMA  739 (910)
Q Consensus       687 v~~~~~~~~Ii-l~T~--~G~~lrF~~~evr---~~~GR~a~GVkgIkL~~~D~Vv~~~  739 (910)
                      +.-+.+++.++ -.|.  ..++..|+  +.+   ++.| -.+||-..+..+.|++++-+
T Consensus       468 ~Vaia~ndkLiAT~SqDktaKiW~le--~~~l~~vLsG-H~RGvw~V~Fs~~dq~laT~  523 (775)
T KOG0319         468 CVAIAPNDKLIATGSQDKTAKIWDLE--QLRLLGVLSG-HTRGVWCVSFSKNDQLLATC  523 (775)
T ss_pred             CEEECCCCCEEEECCCCCCEEEECCC--CCEEEEEEEC-CCCCEEEEEECCCCCEEEEC
T ss_conf             36856877357851666523100146--7638999607-75515888963534045761


No 180
>PRK00969 hypothetical protein; Provisional
Probab=31.41  E-value=26  Score=12.91  Aligned_cols=171  Identities=15%  Similarity=0.152  Sum_probs=76.4

Q ss_pred             CCEEEEEEHHHCCC----CCCCCCCCEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCC
Q ss_conf             98599975876235----478665535767528998699989733666542000001222333333345554--444444
Q gi|254780182|r  702 LGQCVRFPISAIRV----FAGRNSVGVRGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDT--EEITSL  775 (910)
Q Consensus       702 ~G~~lrF~~~evr~----~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~  775 (910)
                      .|++-.+.++-...    .-||...|...+++.+.-..++....+.--.     ...+....+....+...+  ......
T Consensus       272 ~G~vYIYredr~ss~sHtvVG~V~~GiELid~a~~G~~itv~t~Peri~-----llG~t~~eA~~~~~~~gIe~~~dg~~  346 (508)
T PRK00969        272 VGKVYIYREDRPSSLSHTVVGRVTHGIELVDFAEEGDRLTVKTVPERLD-----LLGLTLKEAEELLEKLGIELEKDGYT  346 (508)
T ss_pred             CEEEEEECCCCCCCCCCCEEEEEECCEEEEECCCCCCEEEEEECCHHHE-----ECCCCHHHHHHHHHHCCCEEEECCCC
T ss_conf             4469998678788766204678803523320305787799995746714-----22898999999998669689844777


Q ss_pred             CCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEE--------HHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEEC
Q ss_conf             43332222232001110125686799997599345301--------7884866757741488760677776868999972
Q gi|254780182|r  776 KNDSSVEGNISEERCQELKLKEQFILTVSEKGFGKRTS--------SYDFRISNRSGKGIRATDVSKINEIGALVAVFPV  847 (910)
Q Consensus       776 ~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~--------~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V  847 (910)
                      ..++.+....+...+.-++...-.+..|.........-        +.=||.    ..|++.      .+.|.|---|..
T Consensus       347 ~~daVVV~Q~P~~TldIL~~~kV~~~~i~~~~li~IeLydd~AP~s~~yFR~----~tGL~~------~~VG~L~v~F~~  416 (508)
T PRK00969        347 GEDAVVVEQDPPTTLDILKEGKVTTKGIPPDKLIEIELYDDKAPRSVWYFRK----VTGLKT------KPVGKLPVHFKY  416 (508)
T ss_pred             CCCCEEEECCCCHHHHHHHCCCEEEEEECHHHEEEEEECCCCCCHHHHHHHH----HCCCCC------CCCCEEEEEEEE
T ss_conf             8983899658951787751581799961868779999746578357899988----508752------436615889985


Q ss_pred             CCCCEEEEE-ECCCEE----------EEEECCCCCCC--CCCCCCCEEEEECCCCE
Q ss_conf             899649999-459989----------99990105544--51568738898089987
Q gi|254780182|r  848 NDNDQIILV-SDKGTL----------IRVPVNEIRIA--SRATKGVVIFSTAKDER  890 (910)
Q Consensus       848 ~~~DeIlli-T~~G~i----------iR~~v~~I~~~--gR~a~GV~i~~L~~~D~  890 (910)
                      +   +++|+ .+....          -++++.+|-++  .|-..|.--++|.++|+
T Consensus       417 ~---d~~lFk~~~~~~k~liPEN~P~~~V~ag~IgvTN~a~k~~G~iGVRl~d~de  469 (508)
T PRK00969        417 D---DIVLFKGNIEYSKGLIPENTPEDKVEAGEIGVTNMAAKYVGMIGVRLEDNDE  469 (508)
T ss_pred             C---CEEEECCCCHHCCCCCCCCCCCCCCCCCEEEEEEHHHHCCCEEEEEECCCCC
T ss_conf             8---7799747803224568888887753045676660145428657998057754


No 181
>pfam08657 DASH_Spc34 DASH complex subunit Spc34. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules.
Probab=31.33  E-value=26  Score=12.89  Aligned_cols=26  Identities=23%  Similarity=0.231  Sum_probs=19.1

Q ss_pred             HHHHHHCCCCCHHHHHHHCCCCCCCC
Q ss_conf             98876187768888886345866887
Q gi|254780182|r  202 CVAVIDNPDIDLDALMEIIRGPDFPT  227 (910)
Q Consensus       202 ~~~~i~~p~~~~~eL~~~i~GPDFPT  227 (910)
                      +..||++++..-.-|.++-|.+-.|+
T Consensus        36 IT~LIRDte~~EraLf~i~~~~~~~~   61 (212)
T pfam08657        36 ITALIRDTEPHERALFKIDPPKKSPR   61 (212)
T ss_pred             HHHHHCCCCHHHHHHHCCCCCCCCCC
T ss_conf             57886289754565514689888766


No 182
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=31.11  E-value=26  Score=12.87  Aligned_cols=42  Identities=10%  Similarity=0.052  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHCCHHHHH
Q ss_conf             9987899998887--99999989999999998875304989999
Q gi|254780182|r  457 ILELRLARLTGLG--RDDIRNELNSLGIEIKECLDILSSRSRLL  498 (910)
Q Consensus       457 ILdMrL~rLt~LE--~~kl~~E~~eL~~~I~~l~~IL~s~~~l~  498 (910)
                      +.++--.+-.+|+  ...+....+++...+.+|+......++..
T Consensus       364 ~~~~~~~~~~klk~~~~~~~~~~~~~~~~~~y~e~~~~~lek~~  407 (564)
T COG1293         364 NAQRYFKKYKKLKGAKVNLDRQLSELKEAIAYYESAKTALEKAE  407 (564)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             57888888866246400276666657789999999999998551


No 183
>PRK07778 consensus
Probab=31.09  E-value=26  Score=12.86  Aligned_cols=13  Identities=15%  Similarity=0.087  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHCCC
Q ss_conf             7899999971220
Q gi|254780182|r   91 AAIYDALARMAQD  103 (910)
Q Consensus        91 ~siy~a~v~maq~  103 (910)
                      ..|-+|+....++
T Consensus        46 ~~i~~a~~~a~~~   58 (386)
T PRK07778         46 EPVRAAAAAALHR   58 (386)
T ss_pred             HHHHHHHHHHHCC
T ss_conf             9999999998634


No 184
>pfam06447 consensus
Probab=31.07  E-value=26  Score=12.86  Aligned_cols=64  Identities=8%  Similarity=0.105  Sum_probs=37.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             236999999999878999988879--9999989999999998875304989999999998999998
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGR--DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKD  510 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~--~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~  510 (910)
                      =.|++.=.++-|.-+.+.|..|+.  .+++.|.+...+.+++.++-|+.-...+..+++++.++..
T Consensus        46 ~~ft~~v~~~ala~qq~~~~~l~kql~~l~~e~~~~~~~~~~~q~~l~~l~qe~~~L~~q~~~~~~  111 (407)
T pfam06447        46 DDFVNKVNQSAIAEQQKTLSEMQKQIRRLRAEREEKERDLDQNQERIASLEQENQQLREQLAAGQA  111 (407)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             765003257799999999999999999999999999887888899999999999999999998872


No 185
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=30.96  E-value=26  Score=12.85  Aligned_cols=34  Identities=21%  Similarity=0.202  Sum_probs=26.6

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHC
Q ss_conf             97367899999998789999981134042556643
Q gi|254780182|r   49 LKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMG   83 (910)
Q Consensus        49 lKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~g   83 (910)
                      |-|-||++|...+++|. +|-|-+-+..-+.+-||
T Consensus         1 LT~rQ~evl~~A~~~GY-fd~PR~~~l~elA~~lg   34 (53)
T pfam04967         1 LTDRQREILRLAYKMGY-FDYPRRVTLKDLAKELG   34 (53)
T ss_pred             CCHHHHHHHHHHHHCCC-CCCCCCCCHHHHHHHHC
T ss_conf             98899999999998689-77887688999999969


No 186
>COG3394 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.78  E-value=26  Score=12.82  Aligned_cols=140  Identities=19%  Similarity=0.180  Sum_probs=58.7

Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHH----------HCCCHHCCC------CCC
Q ss_conf             8973678999999987899999811340425566436688704789999997----------122011156------131
Q gi|254780182|r   48 GLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALAR----------MAQDWSLRL------LLI  111 (910)
Q Consensus        48 GlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~----------maq~~~~r~------pli  111 (910)
                      ||-|-|-+-+-..|+.|...+.-          +|     -++.++-.|.-+          |-=.++.-.      +|+
T Consensus        13 GLs~G~nyGIiea~~~GvvtsTt----------~M-----~n~pa~~hAv~l~k~~p~l~IGlHl~LT~g~Plt~~~~l~   77 (257)
T COG3394          13 GLSKGVNYGIIEAHRTGVVTSTT----------LM-----VNMPAIDHAVALSKKLPALKIGLHLNLTLGKPLTNMPELT   77 (257)
T ss_pred             CCCCCCCHHHHHHHHCCCEECEE----------EC-----CCCCCCHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf             75655205588898679431202----------30-----5886537799987658887511147860367767886656


Q ss_pred             CCCCCCC-C-C-CCCCCCHHHHHHHHHHHHHH--HHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHH
Q ss_conf             4788708-8-7-76972013578999789999--9986307684053306898854850343227321101676101013
Q gi|254780182|r  112 EGQGNFG-S-V-DGDPPAAERYTECRLQKAAH--FLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGM  186 (910)
Q Consensus       112 dg~GnfG-s-~-dgd~~AA~RYte~rl~~~~~--~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGm  186 (910)
                      |-+|-|+ + . .--+-.+.-+-|..-.-.|+  ..++-...     .|.|=+|.+--..+|.-+|-+ .-=+.+.++  
T Consensus        78 ~e~G~~~~~~~~~~~~~~~~~~eeV~~El~aQ~erF~~~~G~-----~PshlDsHhh~h~~P~I~p~v-~rlA~e~~i--  149 (257)
T COG3394          78 DENGEFGLKWYWLRALEGALDLEEVTAELIAQYERFVELFGR-----TPSHLDSHHHVHMFPQIAPIV-ARLAEEYGI--  149 (257)
T ss_pred             CCCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCC-----CCCCCCCCCCCCCCCHHHHHH-HHHHHCCCC--
T ss_conf             899854613454225234999899999999999999998589-----974113543334341478999-999751496--


Q ss_pred             HHCCCCC---CHHHHHHHHHHHHHCCC
Q ss_conf             3178985---47899999988761877
Q gi|254780182|r  187 ATNIPTH---NLGEVVDGCVAVIDNPD  210 (910)
Q Consensus       187 aTnippH---Nl~Ev~~a~~~~i~~p~  210 (910)
                      +--++++   |.+|...++..+.+..+
T Consensus       150 ~lR~~~~~~~~~~~~~~~ir~~~~~f~  176 (257)
T COG3394         150 PLRIDRTWVSNAGELPAGIRSLLEGFL  176 (257)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             201575334566656410578876400


No 187
>KOG3314 consensus
Probab=30.76  E-value=26  Score=12.82  Aligned_cols=38  Identities=24%  Similarity=0.573  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCC
Q ss_conf             36789999999878999998113404255664366887
Q gi|254780182|r   51 PVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPH   88 (910)
Q Consensus        51 pv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPH   88 (910)
                      |+-+-.+-||-.+|-..+-.+.+|----|.|-|-|||-
T Consensus        38 P~Vkfl~~am~k~~c~~~d~~isc~~C~~~~~GGy~~~   75 (194)
T KOG3314          38 PIVKFLMEAMEKSGCRVGDNFISCVVCTGPVAGGYTPG   75 (194)
T ss_pred             CHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCCC
T ss_conf             38999999999738876677457766899756774688


No 188
>pfam05565 Sipho_Gp157 Siphovirus Gp157. This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage.
Probab=30.75  E-value=26  Score=12.82  Aligned_cols=65  Identities=18%  Similarity=0.236  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC-CCEEE-----CC--CCCCCCCCCCCCCCE
Q ss_conf             9989999999998875304989999999998999998405688-33100-----13--434530101456781
Q gi|254780182|r  474 RNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPR-RTRIV-----EG--LLDMEDEDCIVREDM  538 (910)
Q Consensus       474 ~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~R-RT~I~-----~~--~~~i~~EdlI~~E~v  538 (910)
                      +.+.+.+.++++.|.+.-.+-+...+-+++.|......-|..+ +|.+.     ..  ...+.+|++||++-+
T Consensus        53 ea~~~~~k~e~krl~erkk~~enk~~~LK~yl~~~m~~~g~~kikt~~~tis~rk~~~sv~I~de~~iP~ey~  125 (162)
T pfam05565        53 EADIEAIKAEIKRLAERKKSIENKVKRLKDYLEEAMEATGIKKIKTPLFTVSIRKSKPSVEIEDEAKIPAEYF  125 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCEEEEEECCCCCEECCCHHHCCHHHH
T ss_conf             9789999999999999999999899999999999999809867763767999737899132489566889985


No 189
>PRK08760 replicative DNA helicase; Provisional
Probab=30.68  E-value=27  Score=12.81  Aligned_cols=19  Identities=26%  Similarity=0.441  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHHHCCCC
Q ss_conf             9999999899999840568
Q gi|254780182|r  497 LLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       497 l~~iI~~EL~eik~kygd~  515 (910)
                      ....|-.+|+.+.+.++-|
T Consensus       363 ~v~~isr~lK~lAkel~vp  381 (476)
T PRK08760        363 EISEISRSLKGLAKELNVP  381 (476)
T ss_pred             HHHHHHHHHHHHHHHHCCC
T ss_conf             9999999999999997997


No 190
>pfam03853 YjeF_N YjeF-related protein N-terminus.
Probab=30.67  E-value=25  Score=13.05  Aligned_cols=116  Identities=20%  Similarity=0.237  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHH--------------HHHHHHHHHHHHCCCCCCCCEEC
Q ss_conf             7899999971220111561314788708877697201357899--------------97899999986307684053306
Q gi|254780182|r   91 AAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTEC--------------RLQKAAHFLLDDLGKDTVDFRPN  156 (910)
Q Consensus        91 ~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~--------------rl~~~~~~~l~~i~~~tv~~~~n  156 (910)
                      .++++.+.++-.+-..+...+-|.||.|   ||+=++.||--.              .+++-+...++-..+--+.+.+.
T Consensus        14 ~~~a~~i~~~~~~~~~~v~il~G~GNNG---GDGlv~Ar~L~~~g~~V~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (170)
T pfam03853        14 RAVARVIRKLLSPAGKRVLVLCGPGNNG---GDGLAAARHLAQRGYKVTVLLLNPDEKLSEDARRALEIAKKLGGKIVSL   90 (170)
T ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCCCH---HHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCEEEC
T ss_conf             9999999986187788699998799872---8899999999987990799996785559999999999999869967615


Q ss_pred             CCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCC
Q ss_conf             898854850343227321101676101013317898547899999988761877688888863458668874
Q gi|254780182|r  157 YDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTG  228 (910)
Q Consensus       157 ~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTG  228 (910)
                       +....+    +..=+-+.|-|--||  |+...     +++-+..++.+|+..+..       +=.=|-|+|
T Consensus        91 -~~~~~~----~~~~~d~iVDal~G~--Gl~~~-----l~~~~~~~i~~iN~~~~~-------visiDiPSG  143 (170)
T pfam03853        91 -NPDEDL----SKALADLIIDALFGT--GLSRP-----LRGEYAELIEWINASKAP-------VLAVDIPSG  143 (170)
T ss_pred             -CCCCCC----CCCCCCEEEEEEEEC--CCCCC-----CCHHHHHHHHHHHCCCCC-------EEEEECCCC
T ss_conf             -863201----256662899743523--67988-----988999999999738996-------799737887


No 191
>cd04962 GT1_like_5 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=30.58  E-value=27  Score=12.80  Aligned_cols=35  Identities=9%  Similarity=0.079  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999887530498999999999899999840568
Q gi|254780182|r  481 GIEIKECLDILSSRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       481 ~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      .+-.+.+..+|.+++...+.-.+=...+.++|.-+
T Consensus       324 ~~la~~i~~ll~~~~~~~~~~~~a~~~~~~~fs~~  358 (371)
T cd04962         324 EAMAEYALSLLEDDELWQEFSRAARNRAAERFDSE  358 (371)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             99999999997699999999999999999868999


No 192
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=30.55  E-value=27  Score=12.79  Aligned_cols=181  Identities=11%  Similarity=0.093  Sum_probs=76.6

Q ss_pred             HHHHCCCCCCC--CCC-HHHHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHCCC
Q ss_conf             86313754000--897-3678999999987899999811----3404255664366-88704789999997122011156
Q gi|254780182|r   37 ILGRAIPDLRD--GLK-PVHRRILFGMMQMGVEWNKKYV----KCARISGEVMGKY-HPHGNAAIYDALARMAQDWSLRL  108 (910)
Q Consensus        37 I~~RAlPd~rD--GlK-pv~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gky-HPHGd~siy~a~v~maq~~~~r~  108 (910)
                      -|||+|=.--+  ... -..+||+=+|.+||..||..-+    +..+.+|-++-.+ +|+ -+.+...+-+-++..  .|
T Consensus        16 TVSrvLNg~~~~~~Vs~~Tr~rV~~aa~eLgY~Pn~~Ar~L~~~~t~~Igvvvp~~~n~~-~~~l~~~i~~~~~~~--gy   92 (330)
T PRK11303         16 TASYVINGKAKQYRISDKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTS-YARIAKLLEQQARQR--GY   92 (330)
T ss_pred             HHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCEEEEECCCCCCCH-HHHHHHHHHHHHHHC--CC
T ss_conf             998883899988876999999999999996899488898863087776777545444315-678889999999966--98


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCC-CCCEECCCCCCCCHHCCCCCEEEHHH
Q ss_conf             13147887088776972013578999789999998630768405330689885-48503432273211016761010133
Q gi|254780182|r  109 LLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSF-QEPVVLCARYPNVLVNGGGGIAVGMA  187 (910)
Q Consensus       109 plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~-~EP~vlP~~~P~lL~nG~~GIAvGma  187 (910)
                      -++-    + +-+.|+.--.++.        . +|..-.-+-+=..+...... .-....-..+|.++++....-  .-.
T Consensus        93 ~~li----~-~s~~~~~~e~~~~--------~-~l~~~~vdgiIv~~~~~~~~~~~~~l~~~~iPvV~i~~~~~~--~~~  156 (330)
T PRK11303         93 QLLI----A-CSDDQPDNEMQCA--------E-HLLQRQVDALIVATSLPPEHPFYQRLQNDGFPIIALDRALDR--EHF  156 (330)
T ss_pred             EEEE----E-ECCCCHHHHHHHH--------H-HHHHCCCCEEEEECCCCCCCHHHHHHHHCCCCEEEECCCCCC--CCC
T ss_conf             7999----9-4799989999999--------9-999748998999468888629999998469978997256788--889


Q ss_pred             HCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCC-CCCCCCCCCCCHHHHHHHHH
Q ss_conf             17898547899999988761877688888863458-66887443447588999987
Q gi|254780182|r  188 TNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRG-PDFPTGAVILGRTGIKNAYA  242 (910)
Q Consensus       188 TnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~G-PDFPTGG~I~~~~~i~~~y~  242 (910)
                      ..+-+-|-.-...|+.++++...-.+    -||-| |++++.-  .-..|.+++.+
T Consensus       157 ~~V~~d~~~~~~~a~~~L~~~GhrrI----~~i~~~~~~~~~~--~R~~Gf~~al~  206 (330)
T PRK11303        157 TSVVSDDQDAAEMLAESLLKFPAESI----LLLGALPELSVSF--LREQGFRQALK  206 (330)
T ss_pred             CEEEECCHHHHHHHHHHHHHCCCCEE----EEEECCCCCHHHH--HHHHHHHHHHH
T ss_conf             98997219999999999998699979----9996897563799--99999999999


No 193
>COG3959 Transketolase, N-terminal subunit [Carbohydrate transport and metabolism]
Probab=30.54  E-value=27  Score=12.79  Aligned_cols=16  Identities=25%  Similarity=0.399  Sum_probs=12.7

Q ss_pred             CCCCHHHHHHHHHHHC
Q ss_conf             8870478999999712
Q gi|254780182|r   86 HPHGNAAIYDALARMA  101 (910)
Q Consensus        86 HPHGd~siy~a~v~ma  101 (910)
                      ||||.-|+-|-|.-+=
T Consensus        32 H~G~SLS~~eILa~LY   47 (243)
T COG3959          32 HVGGSLSVVEILAVLY   47 (243)
T ss_pred             CCCCCCHHHHHHHHHH
T ss_conf             7576210999999999


No 194
>KOG0275 consensus
Probab=30.34  E-value=27  Score=12.77  Aligned_cols=28  Identities=14%  Similarity=0.268  Sum_probs=11.3

Q ss_pred             CEEEEEECCCCCEEEEEECCCEEEEEEC
Q ss_conf             6899997289964999945998999990
Q gi|254780182|r  840 ALVAVFPVNDNDQIILVSDKGTLIRVPV  867 (910)
Q Consensus       840 ~lv~~~~V~~~DeIlliT~~G~iiR~~v  867 (910)
                      ..+++..-.-++.++.+-..|.+.-+.+
T Consensus       439 dFi~~~lSpkGewiYcigED~vlYCF~~  466 (508)
T KOG0275         439 DFINAILSPKGEWIYCIGEDGVLYCFSV  466 (508)
T ss_pred             CEEEEEECCCCCEEEEECCCCEEEEEEE
T ss_conf             5578884488748999736857999996


No 195
>PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated
Probab=30.25  E-value=27  Score=12.76  Aligned_cols=70  Identities=17%  Similarity=0.165  Sum_probs=44.8

Q ss_pred             HHHHHHHHHC--CCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998618--99789878776312697889999974022111222344523699999999987899998887999999
Q gi|254780182|r  398 DEVVRIIRFS--PNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRN  475 (910)
Q Consensus       398 DeVI~iIR~S--~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~  475 (910)
                      ++.|+=||.+  +-|++-+.+|++.                          |+||+.+|+.+++=+.          + +
T Consensus       443 ~e~Ie~Ik~~LPELP~~kr~Rl~~e--------------------------ygLs~~dA~~L~~~~~----------l-~  485 (631)
T PRK04028        443 EELLEKIKKNLPELPEEKLERLVKE--------------------------YGLSEELAEQLANSER----------L-D  485 (631)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHH--------------------------CCCCHHHHHHHHCCCH----------H-H
T ss_conf             9999999971899999999999997--------------------------0989999999974738----------9-9


Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999988753049899999999989999984
Q gi|254780182|r  476 ELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDE  511 (910)
Q Consensus       476 E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~k  511 (910)
                      .++++.+       .-.+++..-+.+...|.+++++
T Consensus       486 ~FE~~v~-------~~~~pk~~An~l~~~l~~L~~~  514 (631)
T PRK04028        486 LFEELVK-------KGVKPTLIARTLVNTLKELKRE  514 (631)
T ss_pred             HHHHHHH-------CCCCHHHHHHHHHHHHHHHHHC
T ss_conf             9999997-------1699999999999999999976


No 196
>pfam11629 Mst1_SARAH C terminal SARAH domain of Mst1. This family of proteins represents the C terminal SARAH domain of Mst1. SARAH controls apoptosis and cell cycle arrest via the Ras, RASSF, MST pathway. The Mst1 SARAH domain interacts with Rassf1 and Rassf5 by forming a heterodimer which mediates the apoptosis process.
Probab=30.15  E-value=27  Score=12.74  Aligned_cols=32  Identities=19%  Similarity=0.228  Sum_probs=21.3

Q ss_pred             HHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             88753049899999999989999984056883310
Q gi|254780182|r  486 ECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI  520 (910)
Q Consensus       486 ~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I  520 (910)
                      +|+.-|+|   +..-+-.|+.+++.+|..+|.-.+
T Consensus        12 eL~~rl~s---LD~~ME~Eieelr~RYq~KRqPIL   43 (49)
T pfam11629        12 ELEQRLAS---LDPEMETEIEELRQRYQAKRQPIL   43 (49)
T ss_pred             HHHHHHHH---CCHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             99999986---678899999999999887424399


No 197
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=30.05  E-value=27  Score=12.73  Aligned_cols=14  Identities=21%  Similarity=0.382  Sum_probs=7.2

Q ss_pred             CCCCEEEEEEEECC
Q ss_conf             89986999897336
Q gi|254780182|r  730 AKGDQVISMAIVLH  743 (910)
Q Consensus       730 ~~~D~Vv~~~vi~~  743 (910)
                      ..+++|.|+.+.+.
T Consensus       202 ~~~~~VRGiLvAp~  215 (253)
T COG1637         202 DTGDKVRGILVAPS  215 (253)
T ss_pred             CCCCEEEEEEECCC
T ss_conf             46860789998664


No 198
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=29.91  E-value=27  Score=12.71  Aligned_cols=25  Identities=32%  Similarity=0.425  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      |+||+.|-+||++....+|-.+.-+
T Consensus        54 ~~Lteeqk~aV~~RD~~~li~lGgn   78 (129)
T PRK13377         54 WPMTEEQKQAVLARDLNRCIALGGN   78 (129)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             6999999999997379999992673


No 199
>pfam06952 PsiA PsiA protein. This family consists of several Enterobacterial PsiA proteins. The function of PsiA is unknown although it is thought that it may affect the generation of an SOS signal in Escherichia coli.
Probab=29.83  E-value=27  Score=12.70  Aligned_cols=16  Identities=44%  Similarity=0.607  Sum_probs=7.4

Q ss_pred             CCCCCEEEHHHHCCCC
Q ss_conf             1676101013317898
Q gi|254780182|r  177 NGGGGIAVGMATNIPT  192 (910)
Q Consensus       177 nG~~GIAvGmaTnipp  192 (910)
                      ||+.+|-+--+-.|||
T Consensus        49 nGs~rI~~~d~r~i~~   64 (238)
T pfam06952        49 NGSGRINATDARRIPG   64 (238)
T ss_pred             CCCCCCCHHHHHHCCC
T ss_conf             5866442766522587


No 200
>cd04626 CBS_pair_13 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=29.81  E-value=22  Score=13.46  Aligned_cols=27  Identities=19%  Similarity=0.293  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHCCCHHCCCCCCCCCCCC
Q ss_conf             789999997122011156131478870
Q gi|254780182|r   91 AAIYDALARMAQDWSLRLLLIEGQGNF  117 (910)
Q Consensus        91 ~siy~a~v~maq~~~~r~plidg~Gnf  117 (910)
                      +++.+|+-.|.+......|.+|.+|.+
T Consensus        10 ~tl~eA~~~m~~~~~~~~~Vvd~~~~l   36 (111)
T cd04626          10 ASIREALHEMLKYNTNEIIVKDNEEKL   36 (111)
T ss_pred             CCHHHHHHHHHHHCCCEEEEECCCCEE
T ss_conf             939999999998499889999699979


No 201
>TIGR02483 PFK_mixed phosphofructokinase; InterPro: IPR012829    Members of this family that are characterised, save one, are phosphofructokinases dependent on pyrophosphate (2.7.1.90 from EC) rather than ATP (2.7.1.11 from EC). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal.; GO: 0005524 ATP binding, 0008443 phosphofructokinase activity, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=29.78  E-value=27  Score=12.69  Aligned_cols=31  Identities=26%  Similarity=0.617  Sum_probs=23.0

Q ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             678459999246443528999999999987166
Q gi|254780182|r  260 SGDREQIVVTEIPYQVNKAAMLEKIAELVREKR  292 (910)
Q Consensus       260 ~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~k  292 (910)
                      .+|=+-|.|=|+||.++  ++++||.+.-+.+|
T Consensus       197 aGGAd~ILIPE~P~d~~--~v~~~v~~r~~~G~  227 (339)
T TIGR02483       197 AGGADVILIPEIPFDID--SVCEKVRERFARGK  227 (339)
T ss_pred             HCCCCEEEECCCCCCHH--HHHHHHHHHHHCCC
T ss_conf             20876789786048889--99999999987266


No 202
>pfam01768 Birna_VP4 Birnavirus VP4 protein. VP4 is a viral protease. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C).
Probab=29.77  E-value=13  Score=15.62  Aligned_cols=24  Identities=33%  Similarity=0.566  Sum_probs=9.0

Q ss_pred             CCCCCCCCCC-CCCCCCCCCHHHHH
Q ss_conf             6131478870-88776972013578
Q gi|254780182|r  108 LLLIEGQGNF-GSVDGDPPAAERYT  131 (910)
Q Consensus       108 ~plidg~Gnf-Gs~dgd~~AA~RYt  131 (910)
                      -||++--+.| |.+-||.||+-||+
T Consensus        14 APLigaad~~i~~l~~~~Aa~gr~~   38 (264)
T pfam01768        14 APLIGAADQFIGDLLGDNASGGRYV   38 (264)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             2012246666665316633367624


No 203
>KOG4288 consensus
Probab=29.52  E-value=28  Score=12.66  Aligned_cols=35  Identities=31%  Similarity=0.440  Sum_probs=20.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             7898547899999988761877688888863458668874434475889999
Q gi|254780182|r  189 NIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNA  240 (910)
Q Consensus       189 nippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~  240 (910)
                      -+||-|..+|.-|.+.-+.              -|||+  |+ +..++|.++
T Consensus       243 ~~ppvnve~VA~aal~ai~--------------dp~f~--Gv-v~i~eI~~~  277 (283)
T KOG4288         243 LAPPVNVESVALAALKAIE--------------DPDFK--GV-VTIEEIKKA  277 (283)
T ss_pred             CCCCCCHHHHHHHHHHHCC--------------CCCCC--CE-EEHHHHHHH
T ss_conf             4798678999999997424--------------87757--60-559999998


No 204
>KOG3686 consensus
Probab=29.38  E-value=28  Score=12.64  Aligned_cols=22  Identities=14%  Similarity=0.039  Sum_probs=15.1

Q ss_pred             CCCCEEEEEECCCEEEEEEHHH
Q ss_conf             8982699993698599975876
Q gi|254780182|r  691 TQENDILLTTKLGQCVRFPISA  712 (910)
Q Consensus       691 ~~~~~Iil~T~~G~~lrF~~~e  712 (910)
                      ...+.+++++...+...|++..
T Consensus       532 ~~~~~~~~~s~~~~~v~fn~~~  553 (740)
T KOG3686         532 ISPHLDVLSSREVHKVAFNEDR  553 (740)
T ss_pred             CCCCCEEEECCCCCCEEEECCC
T ss_conf             7854124304356625885244


No 205
>PRK13670 hypothetical protein; Provisional
Probab=29.22  E-value=27  Score=12.69  Aligned_cols=120  Identities=17%  Similarity=0.407  Sum_probs=57.7

Q ss_pred             HHHHHHCCCCCCCHHHHHH--HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCE
Q ss_conf             2556643668870478999--99971220111561314788708877697201357899978999999863076840533
Q gi|254780182|r   77 ISGEVMGKYHPHGNAAIYD--ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFR  154 (910)
Q Consensus        77 ivg~v~gkyHPHGd~siy~--a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~  154 (910)
                      +||= +--|.|.-..-.|-  ..-...   .--+..+-.-|||=-. |.||=...|+-|+++     +..+     ||.|
T Consensus         3 ~~GI-IaEYNPFHnGH~Yhi~~ar~~t---~ad~iIaVMSGnFvQR-GEPAi~dKw~Ra~~A-----L~~G-----aDLV   67 (390)
T PRK13670          3 ATGI-IVEYNPFHNGHLYHLNQAKKLT---KADVTIAVMSGNFVQR-GEPAIVDKWTRAKMA-----LANG-----ADLV   67 (390)
T ss_pred             EEEE-EEEECCCCCHHHHHHHHHHHHC---CCCEEEEEECCCCCCC-CCCHHCCHHHHHHHH-----HHCC-----CCEE
T ss_conf             3689-9610797410899999999753---9987999943885108-872007878999999-----9859-----9889


Q ss_pred             ECCCCCCCCCEECCCCCC----CCHHC---------CCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHC-
Q ss_conf             068988548503432273----21101---------6761010133178985478999999887618776888888634-
Q gi|254780182|r  155 PNYDGSFQEPVVLCARYP----NVLVN---------GGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEII-  220 (910)
Q Consensus       155 ~n~D~~~~EP~vlP~~~P----~lL~n---------G~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i-  220 (910)
                      =          =||.-+-    -....         |.+-|+-|+-+.    ++.....+.-.+.++|+.- +++++++ 
T Consensus        68 i----------ELP~~ya~qsAe~FA~gaV~lL~~lgvd~l~FGsE~~----d~~~l~~~a~~l~~~~~~~-~~~~~~L~  132 (390)
T PRK13670         68 V----------ELPFVFAVQSADYFAEGAVSILDALGVDDLVFGSESG----DIEDFQKLAKIINEKPEEF-EAFLKKLK  132 (390)
T ss_pred             E----------ECCHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCC----CHHHHHHHHHHHHHCHHHH-HHHHHHHH
T ss_conf             9----------8865988625999999999999986999899668889----8999999999998680889-99999866


Q ss_pred             CCCCCC
Q ss_conf             586688
Q gi|254780182|r  221 RGPDFP  226 (910)
Q Consensus       221 ~GPDFP  226 (910)
                      +|=-||
T Consensus       133 ~G~Syp  138 (390)
T PRK13670        133 KGLSYP  138 (390)
T ss_pred             CCCCHH
T ss_conf             789999


No 206
>cd04613 CBS_pair_SpoIVFB_EriC_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC.  SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus).  SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB.  It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase a
Probab=29.06  E-value=24  Score=13.22  Aligned_cols=28  Identities=11%  Similarity=0.287  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHCCCHHCCCCCCCCCCCC
Q ss_conf             4789999997122011156131478870
Q gi|254780182|r   90 NAAIYDALARMAQDWSLRLLLIEGQGNF  117 (910)
Q Consensus        90 d~siy~a~v~maq~~~~r~plidg~Gnf  117 (910)
                      |+++.+|+-.|.+.--..+|.+|.+|+|
T Consensus         9 ~~tl~ea~~~m~~~~~~~~pVvd~~~~l   36 (114)
T cd04613           9 DTPLNELLDVIAHSPENNFPVVDDDGRL   36 (114)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEECCCCEE
T ss_conf             0989999999986199789999289949


No 207
>cd04593 CBS_pair_EriC_assoc_bac_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS d
Probab=29.03  E-value=24  Score=13.27  Aligned_cols=26  Identities=12%  Similarity=0.265  Sum_probs=8.9

Q ss_pred             HHHHHHHHHHCCCHHCCCCCCCCCCC
Q ss_conf             78999999712201115613147887
Q gi|254780182|r   91 AAIYDALARMAQDWSLRLLLIEGQGN  116 (910)
Q Consensus        91 ~siy~a~v~maq~~~~r~plidg~Gn  116 (910)
                      ++++||+-.|.+.-....|.+|.+|.
T Consensus        10 ~tv~ea~~~m~~~~~~~~pVvD~~g~   35 (115)
T cd04593          10 TPLREAAEQLIESKHGSALVVDRDGG   35 (115)
T ss_pred             CCHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             99999999998749989999949998


No 208
>smart00116 CBS Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease.
Probab=28.96  E-value=26  Score=12.85  Aligned_cols=30  Identities=17%  Similarity=0.320  Sum_probs=22.8

Q ss_pred             CCHHHHHHHHHHHCCCHHCCCCCCCCCCCC
Q ss_conf             704789999997122011156131478870
Q gi|254780182|r   88 HGNAAIYDALARMAQDWSLRLLLIEGQGNF  117 (910)
Q Consensus        88 HGd~siy~a~v~maq~~~~r~plidg~Gnf  117 (910)
                      +-++++.+|+-.|.+.---+.|.+|.+|+.
T Consensus         6 ~~~~~v~~a~~~m~~~~i~~lPVVd~~~~l   35 (49)
T smart00116        6 SPDTTLEEALELLREHGIRRLPVVDEEGRL   35 (49)
T ss_pred             CCCCCHHHHHHHHHHHCCCEEEEECCCCCE
T ss_conf             987929999999998099857699899919


No 209
>COG3546 Mn-containing catalase [Inorganic ion transport and metabolism]
Probab=28.59  E-value=28  Score=12.54  Aligned_cols=33  Identities=27%  Similarity=0.322  Sum_probs=21.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHH---HHHHHHHCCCC
Q ss_conf             0887769720135789997899---99998630768
Q gi|254780182|r  117 FGSVDGDPPAAERYTECRLQKA---AHFLLDDLGKD  149 (910)
Q Consensus       117 fGs~dgd~~AA~RYte~rl~~~---~~~~l~~i~~~  149 (910)
                      ||-.+|.-+|||||.--+++--   ..+||.||.-+
T Consensus        29 lGG~~GElsaamqYl~Q~fn~r~~~~~dll~DI~TE   64 (277)
T COG3546          29 LGGAFGELSAAMQYLFQGFNVRDAKYKDLLMDIGTE   64 (277)
T ss_pred             HCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             679624799999998753466753799999986478


No 210
>KOG3809 consensus
Probab=28.55  E-value=29  Score=12.53  Aligned_cols=42  Identities=24%  Similarity=0.237  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHCCHHHHHHHHH
Q ss_conf             89999888799999989999999998875--------3049899999999
Q gi|254780182|r  461 RLARLTGLGRDDIRNELNSLGIEIKECLD--------ILSSRSRLLGIIK  502 (910)
Q Consensus       461 rL~rLt~LE~~kl~~E~~eL~~~I~~l~~--------IL~s~~~l~~iI~  502 (910)
                      +=+++|.-..+-|.+++++|++.|+++++        ||+++.++.+.|-
T Consensus       532 ~eq~~t~~a~epL~~~la~lq~~I~d~~e~i~~~r~~IL~Ne~rIqk~i~  581 (583)
T KOG3809         532 NEQAATFGASEPLYNILANLQKEINDTKEEISKARGRILNNEKRIQKFIS  581 (583)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             66531334421799999999999999999999999888504899999974


No 211
>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=28.35  E-value=22  Score=13.52  Aligned_cols=22  Identities=23%  Similarity=0.244  Sum_probs=11.3

Q ss_pred             ECCCCEEEECHHH--HHHCCCCCE
Q ss_conf             4799189842368--620477722
Q gi|254780182|r  652 TKHGNVRRNKLSD--FIQINRSGK  673 (910)
Q Consensus       652 Tk~G~VKkt~l~e--f~~~r~~G~  673 (910)
                      =|+|.++-=|+++  +.-++++-+
T Consensus       196 VK~G~l~TPp~~~s~L~GITRd~V  219 (302)
T TIGR01122       196 VKDGVLITPPVSSSILKGITRDTV  219 (302)
T ss_pred             EECCEEECCCCHHHHCCCCCHHHH
T ss_conf             708678789870422488888899


No 212
>KOG4318 consensus
Probab=28.35  E-value=29  Score=12.50  Aligned_cols=178  Identities=14%  Similarity=0.174  Sum_probs=93.8

Q ss_pred             HHHHHHH----HHHHHHHHHCCC-CCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf             9876787----779988631375-40008973678999999987899999811340425566436688704789999997
Q gi|254780182|r   25 MQNSYLT----YAINVILGRAIP-DLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALAR   99 (910)
Q Consensus        25 m~~syl~----Ya~svI~~RAlP-d~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~   99 (910)
                      |-+||-.    .+.-..+.||+- -.-||-||    +||.|.+-|+ |=++|.=-+=++|        -++.++.+-..|
T Consensus       194 ~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~----ll~emke~gf-pir~HyFwpLl~g--------~~~~q~~e~vlr  260 (1088)
T KOG4318         194 MCKSLVEAPTSETLHAVLKRALAAGDVDGAKN----LLYEMKEKGF-PIRAHYFWPLLLG--------INAAQVFEFVLR  260 (1088)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHH----HHHHHHHCCC-CCCCCCCHHHHHC--------CCCCHHHHHHHH
T ss_conf             99985137881799999999885276144799----9999997688-7651000356616--------764167999999


Q ss_pred             HCCCHHC----------CCCCCCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHH--HHHHCCCCCCCCEECCCCCCCCCE
Q ss_conf             1220111----------56131478870887--769720135789997899999--986307684053306898854850
Q gi|254780182|r  100 MAQDWSL----------RLLLIEGQGNFGSV--DGDPPAAERYTECRLQKAAHF--LLDDLGKDTVDFRPNYDGSFQEPV  165 (910)
Q Consensus       100 maq~~~~----------r~plidg~GnfGs~--dgd~~AA~RYte~rl~~~~~~--~l~~i~~~tv~~~~n~D~~~~EP~  165 (910)
                      |-|.++.          -.|..+   |+-.-  +--.+-+|-.|-+-.+..+..  -..++++++..             
T Consensus       261 gmqe~gv~p~seT~adyvip~l~---N~~t~~~~e~sq~~hg~tAavrsaa~rg~~a~k~l~~nl~~-------------  324 (1088)
T KOG4318         261 GMQEKGVQPGSETQADYVIPQLS---NGQTKYGEEGSQLAHGFTAAVRSAACRGLLANKRLRQNLRK-------------  324 (1088)
T ss_pred             HHHHHCCCCCCCHHHHHHHHHHC---CHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH-------------
T ss_conf             99994678986225778876411---24555222246243323489999996252767789887899-------------


Q ss_pred             ECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCH--HHHHHHHHH
Q ss_conf             343227321101676101013317898547899999988761877688888863458668874434475--889999870
Q gi|254780182|r  166 VLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGR--TGIKNAYAT  243 (910)
Q Consensus       166 vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~--~~i~~~y~t  243 (910)
                      .+|-.+|-+|+-|         |.+|| |..-.|.-.++  ..|.-.++.|...++.|-|---|.-++-  +.++++|.-
T Consensus       325 ~v~~s~k~~fLlg---------~d~~~-aiws~c~~l~h--Qgk~e~veqlvg~l~npt~r~s~~~V~a~~~~lrqyFrr  392 (1088)
T KOG4318         325 SVIGSTKKLFLLG---------TDILE-AIWSMCEKLRH--QGKGEEVEQLVGQLLNPTLRDSGQNVDAFGALLRQYFRR  392 (1088)
T ss_pred             HHHHHHHHHHHHC---------CCCCH-HHHHHHHHHHH--CCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             8787746878860---------45536-89999999997--079851999975652771204751377999999999999


No 213
>PRK08694 consensus
Probab=28.28  E-value=29  Score=12.49  Aligned_cols=23  Identities=35%  Similarity=0.557  Sum_probs=14.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98999999999899999840568
Q gi|254780182|r  493 SRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       493 s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      ++......|-..|+.+.+.++-|
T Consensus       350 ~r~~~i~~isr~LK~lAkel~ip  372 (468)
T PRK08694        350 NRASELGEISRSLKALAKELQVP  372 (468)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             59999999999999999997998


No 214
>pfam12529 Xylo_C Xylosyltransferase C terminal. This domain family is found in eukaryotes, and is typically between 169 and 183 amino acids in length. The family is found in association with pfam02485. There is a single completely conserved residue G that may be functionally important. Xylosyltransferases are enzymes involved in the biosynthesis of the glycosaminoglycan linker region in proteoglycans.
Probab=28.27  E-value=29  Score=12.49  Aligned_cols=41  Identities=17%  Similarity=0.203  Sum_probs=14.8

Q ss_pred             EEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEE
Q ss_conf             79999479918984236862047772278661589857888
Q gi|254780182|r  647 YVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSV  687 (910)
Q Consensus       647 ~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v  687 (910)
                      |||-....+.-++..++-+..++.+++.+=.....-+|..+
T Consensus        85 fLV~~~a~~~~~~~~lE~w~~P~~~~~~~~~~~~~~RL~~~  125 (180)
T pfam12529        85 FLVRFEAQATGQRETLETWVSPQVSLKLARALVLSKRLRNL  125 (180)
T ss_pred             EEEEEEEECCCCCEEEEEEEEECCCEEEECCCCHHCEEEEE
T ss_conf             99999996699722367777400201540585400200466


No 215
>KOG2052 consensus
Probab=28.16  E-value=27  Score=12.73  Aligned_cols=16  Identities=25%  Similarity=0.260  Sum_probs=8.1

Q ss_pred             EEEEECCCEEEEEEHH
Q ss_conf             9999369859997587
Q gi|254780182|r  696 ILLTTKLGQCVRFPIS  711 (910)
Q Consensus       696 Iil~T~~G~~lrF~~~  711 (910)
                      ...+...|.++|++..
T Consensus       354 ~C~IADLGLAv~h~~~  369 (513)
T KOG2052         354 TCCIADLGLAVRHDSD  369 (513)
T ss_pred             CEEEEECEEEEEECCC
T ss_conf             3798603014772366


No 216
>PRK11387 S-methylmethionine transporter; Provisional
Probab=27.76  E-value=29  Score=12.42  Aligned_cols=40  Identities=15%  Similarity=0.085  Sum_probs=18.6

Q ss_pred             HHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             1016761010133178985478999999887618776888
Q gi|254780182|r  175 LVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLD  214 (910)
Q Consensus       175 L~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~  214 (910)
                      +-||..|+..+|+.-.=.+.=-|.+-..-.-.+||.-++.
T Consensus       201 ~~~g~~~i~~~~~~~~faf~G~e~i~~~A~E~knP~r~iP  240 (465)
T PRK11387        201 FPHGTLPILMTMVAVNFAFSGTELIGIAAGETENPAKVIP  240 (465)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHH
T ss_conf             6555899999999999997166999999999718676899


No 217
>TIGR01951 nusB transcription antitermination factor NusB; InterPro: IPR011605   The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. The antitermination proteins of Escherichia coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle. The solution structure indicates that the protein folds into an alpha/alpha-helical topology consisting of six helices; the arginine-rich N-terminus appears to be disordered .; GO: 0003715 transcription termination factor activity, 0006353 transcription termination.
Probab=27.75  E-value=29  Score=12.42  Aligned_cols=54  Identities=13%  Similarity=0.273  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH--HHHHHHHHHHHCCCCCCCEEECC
Q ss_conf             8999988879999998999999999887530498999999--99989999984056883310013
Q gi|254780182|r  461 RLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGI--IKQELLSVKDELDTPRRTRIVEG  523 (910)
Q Consensus       461 rL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~i--I~~EL~eik~kygd~RRT~I~~~  523 (910)
                      +|.||+..|+.=|+=         .-|+-+-...+-=.++  +++|--||.|+||++==.+.+.+
T Consensus        78 ~l~RL~~VdraILRl---------~~yEl~~~~~D~P~~VA~~InEAielAK~ys~~~s~kFiNG  133 (140)
T TIGR01951        78 TLERLSKVDRAILRL---------AAYELLYLKKDVPVKVAVVINEAIELAKKYSDDKSSKFING  133 (140)
T ss_pred             CHHHHHHHHHHHHHH---------HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf             723512878999999---------99999863689894054325789999998426876413787


No 218
>KOG3441 consensus
Probab=27.68  E-value=13  Score=15.52  Aligned_cols=16  Identities=31%  Similarity=0.692  Sum_probs=6.9

Q ss_pred             CCCCEEEEEECCCEEE
Q ss_conf             8996499994599899
Q gi|254780182|r  848 NDNDQIILVSDKGTLI  863 (910)
Q Consensus       848 ~~~DeIlliT~~G~ii  863 (910)
                      .+...+.|+.++|.-+
T Consensus       102 fDsNniVLiddnGnPl  117 (149)
T KOG3441         102 FDSNNIVLIDDNGNPL  117 (149)
T ss_pred             CCCCCEEEECCCCCCC
T ss_conf             1787689987899825


No 219
>pfam05110 AF-4 AF-4 proto-oncoprotein. This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.
Probab=27.59  E-value=29  Score=12.40  Aligned_cols=35  Identities=26%  Similarity=0.428  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999988877----899999987406999999861
Q gi|254780182|r  372 RTKYLLNKARDRAH----VLVGLAIAVANLDEVVRIIRF  406 (910)
Q Consensus       372 Rt~~~L~ka~~R~H----ILeGL~~Al~nIDeVI~iIR~  406 (910)
                      ...|-|..|++-.|    +.+-|-+|+.-+|.|...|.-
T Consensus       909 ~ad~ym~EAKrlKh~Ad~~~dk~gkA~~YldA~lsFiec  947 (1154)
T pfam05110       909 SADYYMQEAKKLKHKADALVDKFGKAVNYLDAVLSFIEC  947 (1154)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             267899999886656778888888999999999999986


No 220
>PRK10803 hypothetical protein; Provisional
Probab=27.51  E-value=30  Score=12.39  Aligned_cols=41  Identities=20%  Similarity=0.134  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999899999999988753049899999999989999984
Q gi|254780182|r  471 DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDE  511 (910)
Q Consensus       471 ~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~k  511 (910)
                      +.++.|..+|+-.|+++..-|..-.+.-+-+-.+|..+...
T Consensus        64 ~~LQ~EV~~LRGqiEe~~~~l~ql~~rQrd~Y~dLD~~~~~  104 (262)
T PRK10803         64 SDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSSG  104 (262)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999999998799999999999999999999999988734


No 221
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=27.48  E-value=30  Score=12.39  Aligned_cols=136  Identities=21%  Similarity=0.368  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHH-----
Q ss_conf             357899978999999863076840533068988548503432273211016761010133178985478999999-----
Q gi|254780182|r  128 ERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGC-----  202 (910)
Q Consensus       128 ~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~-----  202 (910)
                      =||-|. ||.+|-..|..+||=-||++.   |      .=||            ||+=  =+--.||++..+-.+     
T Consensus        49 RRYvES-LSaYARQFLg~~~KPdVD~IE---G------LSPA------------IsId--QKtt~~NPRSTVGTvTEIyD  104 (956)
T TIGR00630        49 RRYVES-LSAYARQFLGVMDKPDVDSIE---G------LSPA------------ISID--QKTTSHNPRSTVGTVTEIYD  104 (956)
T ss_pred             CHHHHH-HHHHHHHHCCCCCCCCCCCCC---C------CCCC------------EEEC--CCCCCCCCCCCCCCEEEHHH
T ss_conf             002100-158999864787477835014---8------8761------------7851--25247888554443210367


Q ss_pred             -----HHHHHC---CC-------CCHHHHHHHCCCCCCCCCC-------CCCCH-----HHHHHHHHHCCCEEEEEEEEE
Q ss_conf             -----887618---77-------6888888634586688744-------34475-----889999870120389999886
Q gi|254780182|r  203 -----VAVIDN---PD-------IDLDALMEIIRGPDFPTGA-------VILGR-----TGIKNAYATGRGSIVIRGVSH  255 (910)
Q Consensus       203 -----~~~i~~---p~-------~~~~eL~~~i~GPDFPTGG-------~I~~~-----~~i~~~y~tGrG~i~iR~k~~  255 (910)
                           -|.+-.   |+       .|.+++..-|  =+.|-|-       ++-++     +-+.++-+.|==+++|-|...
T Consensus       105 YLRLLfArvG~p~CP~~~~~i~~qt~~~Ivd~i--~~~~~g~r~~lLAP~Vr~~KG~f~~~l~~l~~~Gf~RV~vDG~~~  182 (956)
T TIGR00630       105 YLRLLFARVGTPYCPECGRPIEEQTVSQIVDQI--LALPEGTRVILLAPIVRGRKGEFRKLLEKLRKQGFARVRVDGEVY  182 (956)
T ss_pred             HHHHHHHHCCCCCCCCCCCHHHHCCHHHHHHHH--HHCCCCCEEEEECCCCCCCCCCHHHHHHHHHHCCCEEEEECCEEE
T ss_conf             789999836887888777326433878999998--624899658996573247775289999999866961899867788


Q ss_pred             E-EEC------CCCCE--EEEEECCCC--CCCHHHHHHHHHHHHH
Q ss_conf             5-433------67845--999924644--3528999999999987
Q gi|254780182|r  256 I-EKT------SGDRE--QIVVTEIPY--QVNKAAMLEKIAELVR  289 (910)
Q Consensus       256 i-e~~------~~~k~--~ivItEiPY--~vnk~~lie~Ia~lv~  289 (910)
                      - ++.      ++.|.  .+||--|--  .-++.+|.|.|....+
T Consensus       183 ~L~~~~~l~L~k~~KH~I~~ViDR~~v~~~~~~~RL~eSvEtaL~  227 (956)
T TIGR00630       183 RLEDEPTLKLEKNKKHTIDVVIDRLVVKDNENRSRLAESVETALR  227 (956)
T ss_pred             EECCCCCCCCCCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             622132577765555218999824787674332116899999985


No 222
>PRK11622 putative ABC transporter solute-binding protein; Provisional
Probab=27.48  E-value=30  Score=12.39  Aligned_cols=38  Identities=29%  Similarity=0.432  Sum_probs=16.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             7898547899999988761877688888863458668874434475889999
Q gi|254780182|r  189 NIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNA  240 (910)
Q Consensus       189 nippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~  240 (910)
                      .-||.++.|+.+-+.   .||--     +-|-+-||| |     |..=++++
T Consensus       168 ~~pP~s~~eLl~wak---~nPGr-----fTYP~PPdF-~-----GstFlkq~  205 (401)
T PRK11622        168 PQPPQSPAELLEWAK---ANPGR-----FTYPRPPDF-T-----GTAFLKQL  205 (401)
T ss_pred             CCCCCCHHHHHHHHH---HCCCC-----CCCCCCCCC-C-----CHHHHHHH
T ss_conf             999989999999999---78997-----148999987-5-----37999999


No 223
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=27.45  E-value=30  Score=12.38  Aligned_cols=176  Identities=15%  Similarity=0.119  Sum_probs=77.9

Q ss_pred             HHHHCCCCCCCCCCHH-HHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHCCCCC
Q ss_conf             8631375400089736-78999999987899999811----3404255664366-8870478999999712201115613
Q gi|254780182|r   37 ILGRAIPDLRDGLKPV-HRRILFGMMQMGVEWNKKYV----KCARISGEVMGKY-HPHGNAAIYDALARMAQDWSLRLLL  110 (910)
Q Consensus        37 I~~RAlPd~rDGlKpv-~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gky-HPHGd~siy~a~v~maq~~~~r~pl  110 (910)
                      -|||+|=+- .+.+|- ..||+=++.+||..||..-+    +..+++|-++... +|. =+.+..++-+.++.  ..|-+
T Consensus        14 TVSrvLn~~-~~Vs~~tr~rV~~aa~elgY~pn~~Ar~L~~~~s~~Igviv~~~~~~f-~~~i~~~i~~~~~~--~gy~~   89 (327)
T PRK10423         14 TVSHVINKD-RFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPF-YSELVRGVERSCFE--RGYSL   89 (327)
T ss_pred             HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEECCCCCCH-HHHHHHHHHHHHHH--CCCEE
T ss_conf             999997895-999999999999999982998688888775378767999973665512-67889999999998--59989


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC---CEECCCCCCCCCEE---CCCCCCCCHHCCCCCEEE
Q ss_conf             147887088776972013578999789999998630768405---33068988548503---432273211016761010
Q gi|254780182|r  111 IEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVD---FRPNYDGSFQEPVV---LCARYPNVLVNGGGGIAV  184 (910)
Q Consensus       111 idg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~---~~~n~D~~~~EP~v---lP~~~P~lL~nG~~GIAv  184 (910)
                      +-     .+.++|+.-..++.+.        |+.    .-||   +.+.. .....+..   +| .+|.++++...-  -
T Consensus        90 ~l-----~~~~~~~~~~~~~l~~--------l~~----~~vdGiIi~~~~-~~~~~~~~~~~~~-~iP~V~~d~~~~--~  148 (327)
T PRK10423         90 VL-----CNTEGDEQRMNRNLET--------LMQ----KRVDGLLLLCTE-THQPSREIMQRYP-SVPTVMMDWAPF--D  148 (327)
T ss_pred             EE-----EECCCCHHHHHHHHHH--------HHH----CCCCEEEEECCC-CCCHHHHHHHHCC-CCCEEEECCCCC--C
T ss_conf             99-----8268987999999999--------995----598769997477-7762899997279-986899637777--7


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCC-CCCCCCCCCHHHHHHHHHH
Q ss_conf             1331789854789999998876187768888886345866-8874434475889999870
Q gi|254780182|r  185 GMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPD-FPTGAVILGRTGIKNAYAT  243 (910)
Q Consensus       185 GmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPD-FPTGG~I~~~~~i~~~y~t  243 (910)
                      +...-+...|..-.-.|+-++++...-.+    -|+-||. ..+.  -.-.+|.+++.+.
T Consensus       149 ~~~~~v~~d~~~~~~~a~~~L~~~Ghr~I----~~i~~~~~~~~~--~~R~~gf~~al~~  202 (327)
T PRK10423        149 GDSDLIQDNSLLGGDLATQYLIDKGHTRI----ACITGPLDKTPA--RLRLEGYRAAMKR  202 (327)
T ss_pred             CCCCEEEECHHHHHHHHHHHHHHCCCCEE----EEECCCCCCCHH--HHHHHHHHHHHHH
T ss_conf             88888987789999999999997599749----996688766179--9999999999998


No 224
>KOG2911 consensus
Probab=27.41  E-value=30  Score=12.38  Aligned_cols=89  Identities=21%  Similarity=0.142  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             99999987406999999861899789878776312697889999974022111222344523699999999987899998
Q gi|254780182|r  387 LVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLT  466 (910)
Q Consensus       387 LeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt  466 (910)
                      +|-+..++.|++.|+.-|-+|.+.+.   -|.+                           |+-.-.--+|||.    +--
T Consensus       289 ~er~~~~l~~l~~vl~~Id~s~~nkv---vl~A---------------------------yksGs~alK~il~----~~~  334 (439)
T KOG2911         289 LERKVSSLNNLETVLSQIDNSQTNKV---VLQA---------------------------YKSGSEALKAILA----QGG  334 (439)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHH---HHHH---------------------------HHHHHHHHHHHHH----CCC
T ss_conf             99999999999999998876211089---9999---------------------------9976999999985----268


Q ss_pred             HHH-HHHHHHHHHHHHHHHHHHHHHHCCHHHH-----HHHHHHHHHHHH
Q ss_conf             887-9999998999999999887530498999-----999999899999
Q gi|254780182|r  467 GLG-RDDIRNELNSLGIEIKECLDILSSRSRL-----LGIIKQELLSVK  509 (910)
Q Consensus       467 ~LE-~~kl~~E~~eL~~~I~~l~~IL~s~~~l-----~~iI~~EL~eik  509 (910)
                      +-| .+.+-+|..+...+-++.+++|++.-.-     ..-|-+||.++.
T Consensus       335 s~ekVed~Ldev~et~d~~~EV~~~la~~~~~~~d~~de~lEkEL~~L~  383 (439)
T KOG2911         335 STEKVEDVLDEVNETLDRQEEVEDALASYNVNNIDFEDEDLEKELEDLE  383 (439)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             7045999999999988659999999845898887624699999999997


No 225
>PRK02304 adenine phosphoribosyltransferase; Provisional
Probab=27.19  E-value=24  Score=13.22  Aligned_cols=11  Identities=36%  Similarity=0.573  Sum_probs=4.8

Q ss_pred             CCCEEEEEEEE
Q ss_conf             99869998973
Q gi|254780182|r  731 KGDQVISMAIV  741 (910)
Q Consensus       731 ~~D~Vv~~~vi  741 (910)
                      .|-+|+++.++
T Consensus       139 ~ga~v~~~~~l  149 (174)
T PRK02304        139 LGAEVVGAAFV  149 (174)
T ss_pred             CCCEEEEEEEE
T ss_conf             79989999999


No 226
>KOG0533 consensus
Probab=27.17  E-value=30  Score=12.34  Aligned_cols=25  Identities=32%  Similarity=0.486  Sum_probs=13.5

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             5999924644352899999999998
Q gi|254780182|r  264 EQIVVTEIPYQVNKAAMLEKIAELV  288 (910)
Q Consensus       264 ~~ivItEiPY~vnk~~lie~Ia~lv  288 (910)
                      ..+.|..+||+|.-+.|-|-.++.+
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~  108 (243)
T KOG0533          84 TKVNVSNLPYGVIDADLKELFAEFG  108 (243)
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHC
T ss_conf             2024415886733588999998731


No 227
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase family protein; InterPro: IPR005720   Dihydroorotate dehydrogenase (1.3.3.1 from EC) (DHOdehase) catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria .    This describes dihydroorotate dehydrogenases subfamily 1 that includes a number of uncharacterised proteins and a domain of dihydropyrimidine dehydrogenase.; GO: 0004158 dihydroorotate oxidase activity, 0006207 'de novo' pyrimidine base biosynthetic process, 0005737 cytoplasm.
Probab=27.15  E-value=30  Score=12.34  Aligned_cols=85  Identities=16%  Similarity=0.386  Sum_probs=49.1

Q ss_pred             CCCCCCCCCCC-CCHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCC-CHHHH----HHHHHHHHHCCCCC
Q ss_conf             58668874434-47588999987012038999988654336784599992464435-28999----99999998716650
Q gi|254780182|r  221 RGPDFPTGAVI-LGRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQV-NKAAM----LEKIAELVREKRIV  294 (910)
Q Consensus       221 ~GPDFPTGG~I-~~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~v-nk~~l----ie~Ia~lv~~~ki~  294 (910)
                      |=|=|+--|+. ...+-++=+++.|=|-|+..+----+...+.  +=-|-|.||+. |-=-|    +|+-        ++
T Consensus        11 kNP~~lASG~~G~~~~~l~~~~~~gaGAVvTKs~g~~pr~Gy~--nPtiVE~~~G~lNAiGL~NPG~e~f--------l~   80 (308)
T TIGR01037        11 KNPVILASGVMGSGVEALRRIDRSGAGAVVTKSIGLEPRPGYR--NPTIVEVPCGLLNAIGLQNPGVEAF--------LE   80 (308)
T ss_pred             CCCCEEECCCCCCCHHHHHHHHCCCCCEEEECCEECCCCCCCC--CCEEEECCCCEEEECCCCCHHHHHH--------HH
T ss_conf             0661022110366288999875058863786213315888544--3807981785575235898217999--------98


Q ss_pred             HHHHHHHHCCCCCEEEEEEEC
Q ss_conf             144587303746557999947
Q gi|254780182|r  295 DIADLRDESDRQGYRVVIELK  315 (910)
Q Consensus       295 gI~dirDeSdr~giRivielK  315 (910)
                      .+.+.++|-|+..+||.+-+=
T Consensus        81 E~~~~~~e~~t~dvr~I~svy  101 (308)
T TIGR01037        81 ELKDVREEVPTHDVRLIASVY  101 (308)
T ss_pred             HHHHHHHCCCCCCEEEEEEEC
T ss_conf             632566438987528999831


No 228
>pfam09517 RE_Eco29kI Eco29kI restriction endonuclease. This family includes the Eco29kI (recognizes and cleaves CCGC^GG ) restriction endonuclease.
Probab=27.14  E-value=24  Score=13.19  Aligned_cols=20  Identities=30%  Similarity=0.707  Sum_probs=9.2

Q ss_pred             HHHHHHHCCC-HHCCCCCCCCCCC
Q ss_conf             9999971220-1115613147887
Q gi|254780182|r   94 YDALARMAQD-WSLRLLLIEGQGN  116 (910)
Q Consensus        94 y~a~v~maq~-~~~r~plidg~Gn  116 (910)
                      ..+|.+|-|+ |+   -+|||-||
T Consensus       102 Ea~LI~~~~P~WN---~~idGFGN  122 (170)
T pfam09517       102 EAALIKLFKPLWN---TVVDGFGN  122 (170)
T ss_pred             HHHHHHHHHHHHH---HHCCCCCC
T ss_conf             9999998527776---30454557


No 229
>cd04621 CBS_pair_8 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=27.02  E-value=30  Score=12.32  Aligned_cols=26  Identities=12%  Similarity=0.376  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHCCCHHCCCCCCCCCCC
Q ss_conf             78999999712201115613147887
Q gi|254780182|r   91 AAIYDALARMAQDWSLRLLLIEGQGN  116 (910)
Q Consensus        91 ~siy~a~v~maq~~~~r~plidg~Gn  116 (910)
                      +++.+|+-.|.+.--.+.|.+|..|.
T Consensus        10 ~tl~ea~~~m~~~~i~~lpVvd~~g~   35 (135)
T cd04621          10 HSLLHVVDEMEKNGVGRVIVVDDNGK   35 (135)
T ss_pred             CCHHHHHHHHHHCCCCEEEEECCCCE
T ss_conf             97999999998749977999959993


No 230
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; InterPro: IPR012684    This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (IPR012686 from INTERPRO). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity.
Probab=26.92  E-value=30  Score=12.31  Aligned_cols=16  Identities=13%  Similarity=0.017  Sum_probs=7.7

Q ss_pred             CCEEEEEECCCCEEEE
Q ss_conf             7739999548939998
Q gi|254780182|r  586 HTSVLFFSSLGFVYKE  601 (910)
Q Consensus       586 ~d~LLfFTs~Gkvy~l  601 (910)
                      -.||.=|++-|++|.+
T Consensus        35 vTWL~P~~pPG~ifal   50 (249)
T TIGR02303        35 VTWLPPVEPPGTIFAL   50 (249)
T ss_pred             CEECCCCCCCCCEEEE
T ss_conf             1226868888605662


No 231
>cd04635 CBS_pair_22 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=26.89  E-value=26  Score=12.83  Aligned_cols=28  Identities=18%  Similarity=0.153  Sum_probs=10.4

Q ss_pred             CHHHHHHHHHHHCCCHHCCCCCCCCCCC
Q ss_conf             0478999999712201115613147887
Q gi|254780182|r   89 GNAAIYDALARMAQDWSLRLLLIEGQGN  116 (910)
Q Consensus        89 Gd~siy~a~v~maq~~~~r~plidg~Gn  116 (910)
                      -|.++.+|+-.|.+.--.+.|.+|.+|+
T Consensus        82 ~~~~l~~a~~~m~~~~i~~lpVvd~~g~  109 (122)
T cd04635          82 PDDSIATAVELMLEHDIGRLPVVNEKDQ  109 (122)
T ss_pred             CCCCHHHHHHHHHHHCCCEEEEECCCCE
T ss_conf             9693999999889809988989937998


No 232
>KOG0005 consensus
Probab=26.87  E-value=23  Score=13.36  Aligned_cols=20  Identities=25%  Similarity=0.642  Sum_probs=16.0

Q ss_pred             CCCCCHHHHHHHHHHHHCCC
Q ss_conf             00897367899999998789
Q gi|254780182|r   46 RDGLKPVHRRILFGMMQMGV   65 (910)
Q Consensus        46 rDGlKpv~Rrily~m~~~~~   65 (910)
                      ..|.-|+|.|++|+-.+++-
T Consensus        33 keGIPp~qqrli~~gkqm~D   52 (70)
T KOG0005          33 KEGIPPQQQRLIYAGKQMND   52 (70)
T ss_pred             HCCCCCHHHHHHHCCCCCCC
T ss_conf             21899166632102300255


No 233
>PRK08227 aldolase; Validated
Probab=26.70  E-value=30  Score=12.28  Aligned_cols=23  Identities=26%  Similarity=0.254  Sum_probs=14.4

Q ss_pred             CCHHHHHHHHCCCCCEEEEEEEC
Q ss_conf             50144587303746557999947
Q gi|254780182|r  293 IVDIADLRDESDRQGYRVVIELK  315 (910)
Q Consensus       293 i~gI~dirDeSdr~giRivielK  315 (910)
                      |+.+..|.+|.++-||-++...-
T Consensus       153 l~~lg~v~~e~~~~GmPlla~~~  175 (291)
T PRK08227        153 IKNIIQLVDAGLRYGMPTMAVTA  175 (291)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             99999999999982998799834


No 234
>pfam11853 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=26.55  E-value=31  Score=12.26  Aligned_cols=20  Identities=20%  Similarity=0.346  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             79999998999999999887
Q gi|254780182|r  469 GRDDIRNELNSLGIEIKECL  488 (910)
Q Consensus       469 E~~kl~~E~~eL~~~I~~l~  488 (910)
                      ++++|++|+++|+++.++++
T Consensus        32 kI~~L~~ql~eLk~~~~~~~   51 (485)
T pfam11853        32 KIEALKKELAELKAQLKDLN   51 (485)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999877


No 235
>TIGR01194 cyc_pep_trnsptr cyclic peptide transporter; InterPro: IPR005898   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. This model describes a family of cyclic peptide transporters in bacteria. Syringomycin is an amphipathic, cyclic lipodepsipeptide when inserted into host causes formation of channels, permeable to a variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.; GO: 0005524 ATP binding, 0015197 peptide transporter activity, 0015833 peptide transport, 0016021 integral to membrane.
Probab=26.52  E-value=31  Score=12.25  Aligned_cols=41  Identities=22%  Similarity=0.298  Sum_probs=22.1

Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCCCEEEEE
Q ss_conf             374655799994798877899999997610110000002455
Q gi|254780182|r  303 SDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFSVNMVAL  344 (910)
Q Consensus       303 Sdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~~N~~aL  344 (910)
                      =||-|..=||.+= -.|.+.+=..+|-.|++-....+-+-||
T Consensus       104 ~~R~~~~~~~~~L-T~DI~~~~~~~l~~~~~~~~~~~~l~~~  144 (555)
T TIGR01194       104 VDRRRAHRLLTLL-TSDIDTLSDFLLIFTTLLVELAVFLFGL  144 (555)
T ss_pred             HHCCCCCCEEEHH-HCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             3105775310002-0454478889987889999999999999


No 236
>PRK05748 replicative DNA helicase; Provisional
Probab=26.45  E-value=31  Score=12.24  Aligned_cols=22  Identities=27%  Similarity=0.448  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             8999999999899999840568
Q gi|254780182|r  494 RSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       494 ~~~l~~iI~~EL~eik~kygd~  515 (910)
                      +......|-..|+.+.+.++-|
T Consensus       336 r~~ev~~isr~lK~lAkel~ip  357 (448)
T PRK05748        336 RQQEVSEISRSLKALAKELKVP  357 (448)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999999999999999996998


No 237
>KOG0216 consensus
Probab=26.40  E-value=31  Score=12.24  Aligned_cols=113  Identities=18%  Similarity=0.170  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCC-----CHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHH----HHHHHHHHCCC
Q ss_conf             86688744344-----7588999987012038999988654336784599992464435289999----99999987166
Q gi|254780182|r  222 GPDFPTGAVIL-----GRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAML----EKIAELVREKR  292 (910)
Q Consensus       222 GPDFPTGG~I~-----~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~li----e~Ia~lv~~~k  292 (910)
                      -|-.|++..+.     ...+.++.-.|=+|+.++|=.|++-....+......-++|-++- ++++    -.=.+||.-|.
T Consensus        65 kP~l~~~~~ss~~r~lyPaEcRqR~~TY~Gkl~v~v~wsVNg~~~~~e~~dlG~vPIMlr-SklChL~g~sp~eLV~hkE  143 (1111)
T KOG0216          65 KPMLSDKVHSSDTRKLYPAECRQRGLTYKGKLVVRVSWSVNGGHVVIEKRDLGHVPIMLR-SKLCHLNGASPKELVKHKE  143 (1111)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHCCCEECCEEEEEEEEEECCEEEEEEEEECCCCCEEEE-CCCCCCCCCCHHHHHHCCC
T ss_conf             887786641101220055667645660300499999999888553235543476656876-1535668989589863567


Q ss_pred             ----------CCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCCCEEEE
Q ss_conf             ----------501445873037465579999479887789999999761011000000245
Q gi|254780182|r  293 ----------IVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFSVNMVA  343 (910)
Q Consensus       293 ----------i~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~~N~~a  343 (910)
                                +.||..+        +|.+|-.|||.-...+-+..-..++.-+.|++-|-|
T Consensus       144 e~~EmGGYFIvNGIEKv--------IRmLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRc  196 (1111)
T KOG0216         144 ESSEMGGYFIVNGIEKV--------IRMLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRC  196 (1111)
T ss_pred             CHHHCCCEEEECCHHHH--------HHHHEECCCCCCEEEECHHHHHCCCCCCCCCEEEEE
T ss_conf             65441858998174773--------632010357896578424255357772102369988


No 238
>COG4746 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.35  E-value=31  Score=12.23  Aligned_cols=28  Identities=29%  Similarity=0.616  Sum_probs=17.2

Q ss_pred             HHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCC
Q ss_conf             88886345866887443447588999987012
Q gi|254780182|r  214 DALMEIIRGPDFPTGAVILGRTGIKNAYATGR  245 (910)
Q Consensus       214 ~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGr  245 (910)
                      ++|..+.+|-|||    |.+..++..|.-.|-
T Consensus        10 ~qiv~~~k~a~fP----Inn~~eL~~ALP~G~   37 (80)
T COG4746          10 EQIVEALKGADFP----INNPEELVAALPSGP   37 (80)
T ss_pred             HHHHHHHCCCCCC----CCCHHHHHHHCCCCC
T ss_conf             9999997247877----799899997666899


No 239
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=26.26  E-value=31  Score=12.22  Aligned_cols=28  Identities=11%  Similarity=0.279  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEECC
Q ss_conf             9999999989999984056883310013
Q gi|254780182|r  496 RLLGIIKQELLSVKDELDTPRRTRIVEG  523 (910)
Q Consensus       496 ~l~~iI~~EL~eik~kygd~RRT~I~~~  523 (910)
                      .=..++++|--++.++|+++.-..++..
T Consensus        96 ~p~~v~InE~v~lak~~~~~~~~~fVNg  123 (132)
T PRK00202         96 VPYKVVINEAIELAKKFGDEDSHKFVNG  123 (132)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCHHHHH
T ss_conf             7547799999999999778972133699


No 240
>KOG0977 consensus
Probab=26.22  E-value=31  Score=12.21  Aligned_cols=46  Identities=20%  Similarity=0.238  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             9998999999999887530498999999999899999840568833
Q gi|254780182|r  473 IRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRT  518 (910)
Q Consensus       473 l~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT  518 (910)
                      .++|...+...|..|..=|++-+.....+-+.+..++..-.+++|.
T Consensus       294 ~rEEl~~~R~~i~~Lr~klselE~~n~~L~~~I~dL~~ql~e~~r~  339 (546)
T KOG0977         294 AREELRRIRSRISGLRAKLSELESRNSALEKRIEDLEYQLDEDQRS  339 (546)
T ss_pred             HHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             7899999971021011001130125735898988988654312123


No 241
>PRK06835 DNA replication protein DnaC; Validated
Probab=26.08  E-value=31  Score=12.22  Aligned_cols=20  Identities=15%  Similarity=0.235  Sum_probs=11.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             09999987678777998863
Q gi|254780182|r   20 SITDEMQNSYLTYAINVILG   39 (910)
Q Consensus        20 ~~~~~m~~syl~Ya~svI~~   39 (910)
                      +|.+++...=+.+|...+.+
T Consensus        40 eid~ei~~~~~~~a~~~l~~   59 (330)
T PRK06835         40 EIDREIAKLGIKLSQLILKG   59 (330)
T ss_pred             HHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999998659


No 242
>PRK02753 DNA-directed RNA polymerase subunit omega; Provisional
Probab=25.83  E-value=31  Score=12.16  Aligned_cols=14  Identities=21%  Similarity=0.468  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999998887
Q gi|254780182|r  371 RRTKYLLNKARDRA  384 (910)
Q Consensus       371 rRt~~~L~ka~~R~  384 (910)
                      +|++..++.+..|-
T Consensus        13 ~raE~Li~aasNRY   26 (74)
T PRK02753         13 KRAESLIRASSNRY   26 (74)
T ss_pred             HHHHHHHHHHCCCE
T ss_conf             99999998504544


No 243
>KOG1446 consensus
Probab=25.78  E-value=31  Score=12.15  Aligned_cols=72  Identities=17%  Similarity=0.047  Sum_probs=39.4

Q ss_pred             HHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCEEEEECC-CCCCCCCEEEEEECCCCCEEEEEECCCEEEEEEC
Q ss_conf             111012568679999759934530178848667577414887606-7777686899997289964999945998999990
Q gi|254780182|r  789 RCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGKGIRATDVS-KINEIGALVAVFPVNDNDQIILVSDKGTLIRVPV  867 (910)
Q Consensus       789 ~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~-~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v  867 (910)
                      ...+.++++.+||+-|.+|+-...  +.|+-+       .--.++ +.+...-=..+.-..+..-||.-+..|.+.--++
T Consensus       191 ~~l~FS~dGK~iLlsT~~s~~~~l--DAf~G~-------~~~tfs~~~~~~~~~~~a~ftPds~Fvl~gs~dg~i~vw~~  261 (311)
T KOG1446         191 TDLEFSPDGKSILLSTNASFIYLL--DAFDGT-------VKSTFSGYPNAGNLPLSATFTPDSKFVLSGSDDGTIHVWNL  261 (311)
T ss_pred             EEEEECCCCCEEEEEECCCCEEEE--ECCCCC-------EEEEEEECCCCCCCCEEEEECCCCCEEEEECCCCCEEEEEC
T ss_conf             443875998789998089728999--714870-------74557624678886411798789748998658980899976


Q ss_pred             CC
Q ss_conf             10
Q gi|254780182|r  868 NE  869 (910)
Q Consensus       868 ~~  869 (910)
                      +.
T Consensus       262 ~t  263 (311)
T KOG1446         262 ET  263 (311)
T ss_pred             CC
T ss_conf             78


No 244
>pfam05636 DUF795 Protein of unknown function (DUF795). This family consists of several bacterial proteins of unknown function.
Probab=25.74  E-value=31  Score=12.14  Aligned_cols=122  Identities=17%  Similarity=0.342  Sum_probs=57.9

Q ss_pred             HHHHHHCCCCCCCHHHHH--HHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCE
Q ss_conf             255664366887047899--999971220111561314788708877697201357899978999999863076840533
Q gi|254780182|r   77 ISGEVMGKYHPHGNAAIY--DALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFR  154 (910)
Q Consensus        77 ivg~v~gkyHPHGd~siy--~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~  154 (910)
                      +||= +--|.|.-..-.|  ...-...   .-.+..+-.-|||=-. |.||=...|+-|+++     +..+     ||.|
T Consensus         3 ~~GI-IaEYNPFHnGH~Yhi~~ar~~~---~~d~iIavMSGnFvQR-GEPAi~dKw~Ra~~A-----L~~G-----aDLV   67 (389)
T pfam05636         3 ATGI-IVEYNPFHNGHLYHLNEAKKLT---KADVKIAVMSGNFVQR-GEPAIIDKWERAKMA-----LSSG-----ADLV   67 (389)
T ss_pred             EEEE-EEEECCCCCHHHHHHHHHHHHC---CCCEEEEEECCCCCCC-CCCHHCCHHHHHHHH-----HHCC-----CCEE
T ss_conf             3689-9610797401899999999864---9985999944885218-862007888999999-----9849-----9989


Q ss_pred             ECCCCCCCCCEECCCCCC-------------CCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHC-
Q ss_conf             068988548503432273-------------211016761010133178985478999999887618776888888634-
Q gi|254780182|r  155 PNYDGSFQEPVVLCARYP-------------NVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEII-  220 (910)
Q Consensus       155 ~n~D~~~~EP~vlP~~~P-------------~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i-  220 (910)
                      =          =||..+-             .|=--|.+-+.-|+-|.    |+..+.++.-.+.++|+---+.|-+++ 
T Consensus        68 i----------ELP~~ya~qsAe~FA~gaV~lL~~lgvd~l~FGsE~~----d~~~l~~~a~~l~~~~~~~~~~lk~~l~  133 (389)
T pfam05636        68 I----------ELPVTYSTQSADIFAEGAVSILDSLGIDTLAFGSEEG----DIEDLKKIAKIYLEKEAEMESSLKELLK  133 (389)
T ss_pred             E----------ECCHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCC----CHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_conf             9----------8865988615999999999999986999899658889----8999999999998681889999999987


Q ss_pred             CCCCCCC
Q ss_conf             5866887
Q gi|254780182|r  221 RGPDFPT  227 (910)
Q Consensus       221 ~GPDFPT  227 (910)
                      +|=-||.
T Consensus       134 ~G~Syp~  140 (389)
T pfam05636       134 KGLSYPR  140 (389)
T ss_pred             CCCCHHH
T ss_conf             7999999


No 245
>TIGR03531 selenium_SpcS O-phosphoseryl-tRNA(Sec) selenium transferase. In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein.
Probab=25.72  E-value=32  Score=12.14  Aligned_cols=98  Identities=19%  Similarity=0.277  Sum_probs=56.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH---HHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf             99876787779988631375400089736789999---999878999998113404255664366887047899999971
Q gi|254780182|r   24 EMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILF---GMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARM  100 (910)
Q Consensus        24 ~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily---~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~m  100 (910)
                      +..++....--...-.|.+|+  +|+--.+=-.|.   |+++.++.++     .   ||  .|    --++-||-.||+-
T Consensus        12 ~a~~~~~~~i~~LL~qrklPe--~Gw~d~~Ie~lL~~Ls~mDsNNf~~-----~---vg--vG----EREgRv~s~LV~r   75 (444)
T TIGR03531        12 LVLNAHEKLIERLLEQRKIPE--EGWDDETIELFLSELSVMDTNNFPN-----N---VG--VG----EREGRVFSKLVER   75 (444)
T ss_pred             HHHHHHHHHHHHHHHCCCCCC--CCCCHHHHHHHHHHHHHHCCCCCCC-----C---CC--CC----CCHHHHHHHHHHH
T ss_conf             999999999999997487986--7899899999999997413268844-----4---77--55----2057787799997


Q ss_pred             CCCHHCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             22011156131478870887-7697201357899978999999863
Q gi|254780182|r  101 AQDWSLRLLLIEGQGNFGSV-DGDPPAAERYTECRLQKAAHFLLDD  145 (910)
Q Consensus       101 aq~~~~r~plidg~GnfGs~-dgd~~AA~RYte~rl~~~~~~~l~~  145 (910)
                      -     .|-+-.|=|-=|.+ +--|-||---.=++|+   ..|+.|
T Consensus        76 r-----hy~f~HGIGRSGdl~~~QPKAaGSSll~kLT---n~l~ld  113 (444)
T TIGR03531        76 R-----HYGFCHGIGRSGDLVAPQPKAAGSSLLYKLT---NKLVKD  113 (444)
T ss_pred             H-----HCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH---HHHHHH
T ss_conf             6-----0376667787555465687762328999999---999999


No 246
>pfam10985 DUF2805 Protein of unknown function (DUF2805). This is a bacterial family of proteins with unknown function.
Probab=25.69  E-value=32  Score=12.14  Aligned_cols=38  Identities=16%  Similarity=0.193  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             6999999861899789878776312697889999974022111222344523699999999987899
Q gi|254780182|r  397 LDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLA  463 (910)
Q Consensus       397 IDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~  463 (910)
                      ||+||++-=.-..+=||....                             |+|+|.|+..|.--.|.
T Consensus         1 i~riIeMAweDrt~FeaI~~~-----------------------------~gl~E~eVi~lMR~~Lk   38 (73)
T pfam10985         1 ISRIIEMAWEDRTPFEAIERQ-----------------------------FGLSEKEVIKLMRRELK   38 (73)
T ss_pred             CHHHHHHHHCCCCCHHHHHHH-----------------------------HCCCHHHHHHHHHHHCC
T ss_conf             939999998269989999999-----------------------------89599999999996537


No 247
>KOG4437 consensus
Probab=25.67  E-value=32  Score=12.13  Aligned_cols=15  Identities=13%  Similarity=0.250  Sum_probs=6.4

Q ss_pred             CHHHHHHHHHHHCCH
Q ss_conf             778999999976101
Q gi|254780182|r  319 SADVILNQLYRYTSL  333 (910)
Q Consensus       319 ~~~~vln~Lyk~T~L  333 (910)
                      +++.-.|..|+.-.+
T Consensus       149 ~~~SkFN~F~ef~ki  163 (482)
T KOG4437         149 DPRSKFNLFREFRKL  163 (482)
T ss_pred             CCHHHHHHHHHHHHH
T ss_conf             841022789999999


No 248
>TIGR01363 strep_his_triad streptococcal histidine triad protein; InterPro: IPR006270   The sequences represented in this group are identified by a domain which consists of the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Additional copies of the repeats are found in more poorly conserved regions. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice . .
Probab=25.67  E-value=32  Score=12.13  Aligned_cols=163  Identities=20%  Similarity=0.295  Sum_probs=78.9

Q ss_pred             CCCCCCCCCCCCEEEEEECCCEEC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEEC
Q ss_conf             453010145678189990797052-----------331000002334565211000146410101133237773999954
Q gi|254780182|r  526 DMEDEDCIVREDMVVTVSHLGYVK-----------RVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSS  594 (910)
Q Consensus       526 ~i~~EdlI~~E~vvV~lS~~GyIK-----------r~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs  594 (910)
                      +++.++=|.-|.+||=+|.+|||-           ++|-+.-=+.--==+ -=--+||+.|.|..+.-+      .++-=
T Consensus        61 ~vS~~EGI~AEQIViKITDQGYVTSHGDHYHyYNGKVPYDAIISEELLM~-DPNY~lK~~DivNEi~~G------YVIKV  133 (376)
T TIGR01363        61 EVSKREGINAEQIVIKITDQGYVTSHGDHYHYYNGKVPYDAIISEELLMK-DPNYRLKDSDIVNEIKGG------YVIKV  133 (376)
T ss_pred             HHHHHHCCCCCEEEEEEECCCEECCCCCEEEEECCCCCCHHHHHHHHHCC-CCCCCCCCCCCEEEECCC------EEEEE
T ss_conf             67676288712378997057603136860143278556313221366437-887344643200220386------68988


Q ss_pred             CCCEEE----------EEC-----CCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEE
Q ss_conf             893999----------820-----00432244456554124545365562002566301256668717999947991898
Q gi|254780182|r  595 LGFVYK----------EKV-----WRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRR  659 (910)
Q Consensus       595 ~Gkvy~----------l~v-----~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKk  659 (910)
                      .|+.|.          ++.     -+..+.+...++.-+.++..|...+ +.|+- .    ...+..|   .|.+|+|  
T Consensus       134 ~G~YYVYLK~aa~~~NiRTK~~I~~Q~~~~~~~~~~~Glaqvahl~~~~-~~AV~-~----A~~QGRY---TTDDGYI--  202 (376)
T TIGR01363       134 NGKYYVYLKDAAHADNIRTKEEIARQKQERSKEAKEKGLAQVAHLSKRE-DAAVA-E----ARRQGRY---TTDDGYI--  202 (376)
T ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEHHHHCHHH-HHHHH-H----HHHCCCC---CCCCCCE--
T ss_conf             5818896172122101301789999987433433225401011203246-78999-9----9847881---0457622--


Q ss_pred             ECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCC----CCCCCCCCEE
Q ss_conf             42368620477722786615898578889618982699993698599975876235----4786655357
Q gi|254780182|r  660 NKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRV----FAGRNSVGVR  725 (910)
Q Consensus       660 t~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~----~~GR~a~GVk  725 (910)
                      ++.++...           +-|    .|-++..++|.=-+-++-    .+.+|+-+    ..||..+|.+
T Consensus       203 F~a~DII~-----------D~G----DAY~VPHG~HYHYIPK~~----LSaSELAAA~Ay~s~k~~~~~~  253 (376)
T TIGR01363       203 FNASDIIE-----------DTG----DAYIVPHGDHYHYIPKNE----LSASELAAAEAYWSGKQGRGAR  253 (376)
T ss_pred             ECCHHHHH-----------CCC----CEEECCCCCCCCCCCCCC----CCHHHHHHHHHHHHHCCCCCCC
T ss_conf             27122442-----------178----724604787433367545----7876899999987410466677


No 249
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=25.55  E-value=32  Score=12.12  Aligned_cols=101  Identities=18%  Similarity=0.184  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCC------CCCCCCCCCCCE-EEEEECCCEE
Q ss_conf             899999999988753049899999999989999984056883310013434------530101456781-8999079705
Q gi|254780182|r  476 ELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLD------MEDEDCIVREDM-VVTVSHLGYV  548 (910)
Q Consensus       476 E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~------i~~EdlI~~E~v-vV~lS~~GyI  548 (910)
                      +..++.+++-++..+=..+.+...++++||+.....+-..|.=-|+.....      +-.-.-..+=-. |=-+..+|++
T Consensus         3 ~~~~~LkeL~~~~gpsG~E~eVr~~~~~el~~~~~ev~~D~lGnlia~~~g~~g~~~imi~AHmDEiG~mV~~I~~~G~L   82 (355)
T COG1363           3 ELLELLKELLEAPGPSGYEEEVRDVLKEELEPLGDEVEVDRLGNLIAKKGGKNGPPKVMIAAHMDEIGFMVKEIEDDGFL   82 (355)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCEEECCCCCEEEEECCCCCCCCEEEEEECCEEEEEEEEECCCCEE
T ss_conf             79999999973989998479999999999987087448867873899916889983278986045110378898789659


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEE
Q ss_conf             233100000233456521100014641010113323777399995489399
Q gi|254780182|r  549 KRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVY  599 (910)
Q Consensus       549 Kr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy  599 (910)
                      +-.++--+..|-                       ---+++-++|.+|+-|
T Consensus        83 r~~~iGG~~~~~-----------------------~~gq~v~i~t~~g~~i  110 (355)
T COG1363          83 RFVPIGGWDPQV-----------------------LEGQRVTIHTDKGKKI  110 (355)
T ss_pred             EEEECCCCCHHH-----------------------CCCCEEEEEECCCCEE
T ss_conf             999717967434-----------------------0576799994898687


No 250
>cd04801 CBS_pair_M50_like This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50.  CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=25.29  E-value=31  Score=12.21  Aligned_cols=23  Identities=13%  Similarity=0.193  Sum_probs=7.9

Q ss_pred             HHHHHHHHHCCCHHCCCCCCCCC
Q ss_conf             89999997122011156131478
Q gi|254780182|r   92 AIYDALARMAQDWSLRLLLIEGQ  114 (910)
Q Consensus        92 siy~a~v~maq~~~~r~plidg~  114 (910)
                      ++.+|+-+|.+.---+.|.+|.+
T Consensus        77 ~l~~al~~m~~~~~~~LpVVd~~   99 (114)
T cd04801          77 SLAEVLKLLEEQGLDELAVVEDS   99 (114)
T ss_pred             CHHHHHHHHHHCCCCEEEEECCC
T ss_conf             79999999997698678899479


No 251
>pfam11552 DUF3230 Protein of unknown function (DUF3230). This family of proteins with unknown function appears to be restricted to Streptococcus.
Probab=25.29  E-value=32  Score=12.08  Aligned_cols=21  Identities=38%  Similarity=0.711  Sum_probs=15.1

Q ss_pred             EHHHHCCCCCCHHHHHHHHHHHHHC
Q ss_conf             0133178985478999999887618
Q gi|254780182|r  184 VGMATNIPTHNLGEVVDGCVAVIDN  208 (910)
Q Consensus       184 vGmaTnippHNl~Ev~~a~~~~i~~  208 (910)
                      -|.+|++|+    |+||++-..||+
T Consensus        13 fGvvtSLP~----E~IDs~W~IID~   33 (105)
T pfam11552        13 FGVVTSLPD----EVIDSFWYIIDH   33 (105)
T ss_pred             EEEECCCCH----HHHHHHHHHHHH
T ss_conf             305113988----999999999876


No 252
>PRK08026 flagellin; Validated
Probab=25.27  E-value=32  Score=12.08  Aligned_cols=62  Identities=23%  Similarity=0.308  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             89999998740699999986189978987877631269788999997402211122234452369999999998789999
Q gi|254780182|r  386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL  465 (910)
Q Consensus       386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL  465 (910)
                      -+.||-.|..|.-.-|.+|..+      --.|-+                                .  ..||. |+|-|
T Consensus        57 Qi~GL~qA~rNa~DgiSliQTA------EGAL~e--------------------------------v--~~iLq-RmREL   95 (566)
T PRK08026         57 NIKGLTQAARNANDGISVAQTT------EGALSE--------------------------------I--NNNLQ-RIREL   95 (566)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH------HHHHHH--------------------------------H--HHHHH-HHHHH
T ss_conf             9988999998698899999999------999999--------------------------------9--99999-99999


Q ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------88879999998999999999887
Q gi|254780182|r  466 ---------TGLGRDDIRNELNSLGIEIKECL  488 (910)
Q Consensus       466 ---------t~LE~~kl~~E~~eL~~~I~~l~  488 (910)
                               +.-+|..|++|.++|.++|.++-
T Consensus        96 AVQAANgTns~~dR~aiQ~Ei~qL~~EIdRIa  127 (566)
T PRK08026         96 TVQAATGTNSDSDLDSIQDEIKSRLDEIDRVS  127 (566)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99860478999999999999999999999888


No 253
>pfam05718 Pox_int_trans Poxvirus intermediate transcription factor. This family consists of several highly related Poxvirus sequences which are thought to be intermediate transcription factors.
Probab=25.25  E-value=32  Score=12.08  Aligned_cols=35  Identities=23%  Similarity=0.253  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999878999988879999998999999999887530
Q gi|254780182|r  451 EVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDIL  491 (910)
Q Consensus       451 e~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL  491 (910)
                      -.||++||.|-..|=..|+...++.      ..+.+|++||
T Consensus       348 V~~a~~il~~M~~rS~~L~~~die~------~sVd~LK~lL  382 (383)
T pfam05718       348 VELAESILKMMAERSAILNALDIET------ASVDELKELL  382 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEE------ECHHHHHHHH
T ss_conf             9999999999999987766436300------0499998653


No 254
>CHL00144 odpB pyruvate dehydrogenase E1 component beta subunit; Validated
Probab=25.22  E-value=26  Score=12.83  Aligned_cols=44  Identities=18%  Similarity=0.071  Sum_probs=24.3

Q ss_pred             EEEEC--CCCCHHHHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHH
Q ss_conf             99947--988778999999976101100000024554166300029999999999
Q gi|254780182|r  311 VIELK--RGASADVILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVA  363 (910)
Q Consensus       311 vielK--r~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~  363 (910)
                      ||.++  +-.|.+.|++. -++|.        -+..++.-+...|+-.-+.+.+.
T Consensus       232 VIDlrtl~PlD~e~I~~s-v~kT~--------rlv~veE~~~~gG~Gsei~a~i~  277 (326)
T CHL00144        232 VIDLISLKPLDMTTISTS-IKKTH--------KVLIVEECMKTGGIGAELLALIN  277 (326)
T ss_pred             EEECCCCCCCCHHHHHHH-HHHCC--------CEEEEECCCCCCCHHHHHHHHHH
T ss_conf             986045799999999999-98549--------89999769988978999999999


No 255
>pfam10480 ICAP-1_inte_bdg Beta-1 integrin binding protein. ICAP-1 is a serine/threonine-rich protein that binds to the cytoplasmic domains of beta-1 integrins in a highly specific manner, binding to a NPXY sequence motif on the beta-1 integrin. The cytoplasmic domains of integrins are essential for cell adhesion, and the fact that phosphorylation of ICAP-1 by interaction with the cell-matrix implies an important role of ICAP-1 during integrin-dependent cell adhesion. Overexpression of ICAP-1 strongly reduces the integrin-mediated cell spreading on extracellular matrix and inhibits both Cdc42 and Rac1. In addition, ICAP-1 induces release of Cdc42 from cellular membranes and prevents the dissociation of GDP from this GTPase. An additional function of ICAP-1 is to promote differentiation of osteoprogenitors by supporting their condensation through modulating the integrin high affinity state,
Probab=25.16  E-value=32  Score=12.06  Aligned_cols=39  Identities=26%  Similarity=0.275  Sum_probs=23.2

Q ss_pred             CCHHHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCC
Q ss_conf             2001110125686799997599345301788486675774
Q gi|254780182|r  786 SEERCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGK  825 (910)
Q Consensus       786 ~~e~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgk  825 (910)
                      .++.++....+++++|-|+.+|+ |.+..++|.+..|-+.
T Consensus        97 qDgKlpFv~~deefil~vSkyGi-KV~~~Dq~dVL~RHpL  135 (200)
T pfam10480        97 QDGKLPFVPGDEEFILGVSKYGI-KVASLDQCDVLHRHAL  135 (200)
T ss_pred             HCCCCCCCCCCCCEEEEECCCCE-EECCCHHHHHHHHCCH
T ss_conf             65887755788404787501354-7514335657774334


No 256
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=25.16  E-value=32  Score=12.06  Aligned_cols=25  Identities=28%  Similarity=0.210  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789999888799
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRD  471 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~  471 (910)
                      .+-.|+-+..|-+|=|..|..|+..
T Consensus        98 ~~~~EI~S~~IGe~Vm~~Lk~lD~V  122 (149)
T PRK00464         98 SGEREVPSKEIGELVMEELKKLDEV  122 (149)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCE
T ss_conf             3888755999999999988620931


No 257
>TIGR01219 Pmev_kin_ERG8 phosphomevalonate kinase; InterPro: IPR016005    Phosphomevalonate kinase (2.7.4.2 from EC) catalyzes the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the higher eukaryotic form and the ERG8 type . This model represents plant and fungal forms of the ERG8 type of phosphomevalonate kinase..
Probab=25.09  E-value=32  Score=12.05  Aligned_cols=141  Identities=19%  Similarity=0.142  Sum_probs=69.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCE--EECCCC
Q ss_conf             999987899998887999999899999999988-------75304989999999998999998405688331--001343
Q gi|254780182|r  455 RAILELRLARLTGLGRDDIRNELNSLGIEIKEC-------LDILSSRSRLLGIIKQELLSVKDELDTPRRTR--IVEGLL  525 (910)
Q Consensus       455 ~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l-------~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~--I~~~~~  525 (910)
                      +.=|+-.|..|.+     |.+.+.+...+|-+-       +-.|.+..-+++.|++|+.|+++.+..=||.-  |. .+.
T Consensus       346 N~~l~~~L~~L~~-----L~~~H~D~~~~~~~sCsvL~~~~c~l~~~~Pineaiike~~E~r~a~~~IRr~~r~it-~ea  419 (499)
T TIGR01219       346 NLRLEDKLSDLDK-----LAKDHDDVYLRVIKSCSVLESEDCVLSAEEPINEAIIKELLEVREAVLSIRRLLRKIT-KEA  419 (499)
T ss_pred             HHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH
T ss_conf             6788731347777-----6520013678887652012123503315774578999999999999999999999844-550


Q ss_pred             CCCCCCCCCCCCEEEEEECCCEECC-CCCCCCCCCCCCCCC-CCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEEC
Q ss_conf             4530101456781899907970523-310000023345652-11000146410101133237773999954893999820
Q gi|254780182|r  526 DMEDEDCIVREDMVVTVSHLGYVKR-VPLSVYRAQRRGGKG-RSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKV  603 (910)
Q Consensus       526 ~i~~EdlI~~E~vvV~lS~~GyIKr-~~~~~yr~Q~RggkG-~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v  603 (910)
                      .+++|-...-.=.==+.+-.|=|-. +|-       =||-. ...+...+-|....+..+..         .-+|.++.|
T Consensus       420 ~vdIEP~~QT~lLD~~~~l~GVl~~gvPG-------AGGfDAif~it~~~~d~~~~~~~~w~---------~~~V~~ldV  483 (499)
T TIGR01219       420 KVDIEPEKQTSLLDDIESLEGVLLVGVPG-------AGGFDAIFVITLNDVDLREKVIKAWK---------SDKVLALDV  483 (499)
T ss_pred             CCCCCCHHHHHHHCCCCCCCCEEEEECCC-------CCHHHHHHHHHHCCHHHHHHHHHHHH---------HCCCEEEEE
T ss_conf             78888734433430200258636885289-------85478999887402126889987564---------268347760


Q ss_pred             CCCCCCCCCCCCCC
Q ss_conf             00432244456554
Q gi|254780182|r  604 WRLPIGSPQARGKA  617 (910)
Q Consensus       604 ~~IP~~sr~skG~p  617 (910)
                      .+=|.|-+..+|.|
T Consensus       484 ~~a~~Gv~~E~GDP  497 (499)
T TIGR01219       484 SEADDGVALEKGDP  497 (499)
T ss_pred             CCCCCCCEECCCCC
T ss_conf             45877403168988


No 258
>PRK09492 treR trehalose repressor; Provisional
Probab=25.06  E-value=32  Score=12.05  Aligned_cols=71  Identities=10%  Similarity=0.135  Sum_probs=44.9

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHH-HHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             7779988631375400089736-78999999987899999811----3404255664366887047899999971220
Q gi|254780182|r   31 TYAINVILGRAIPDLRDGLKPV-HRRILFGMMQMGVEWNKKYV----KCARISGEVMGKYHPHGNAAIYDALARMAQD  103 (910)
Q Consensus        31 ~Ya~svI~~RAlPd~rDGlKpv-~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gkyHPHGd~siy~a~v~maq~  103 (910)
                      ..|.+ -|||||=.- .+..|- .+||+=++.+||..|+..-+    +..+++|-|+...+-+.-+.+..++...++.
T Consensus        15 GVS~a-TVSrvLn~~-~~vs~eTr~rV~~~a~elgY~Pn~~Ar~L~~~~t~~Ig~i~~~~~~~~~~~~~~~i~~~~~~   90 (315)
T PRK09492         15 GVGKS-TVSRVLNNE-PKVSPRTRERVEAVINQHGFSPSKSARAMRGQSDKVVGIIVSRLDSPSENLAVQTMLPAFYQ   90 (315)
T ss_pred             CCCHH-HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             97999-999997898-99999999999999999699807788975048886466622677883678999999999997


No 259
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=25.04  E-value=32  Score=12.04  Aligned_cols=52  Identities=12%  Similarity=0.183  Sum_probs=33.6

Q ss_pred             HHHHHHHHHCCCCCCCCCCHH-HHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCC
Q ss_conf             779988631375400089736-78999999987899999811----3404255664366
Q gi|254780182|r   32 YAINVILGRAIPDLRDGLKPV-HRRILFGMMQMGVEWNKKYV----KCARISGEVMGKY   85 (910)
Q Consensus        32 Ya~svI~~RAlPd~rDGlKpv-~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gky   85 (910)
                      .|.+ -|||||=+- .+..|- .+||+=++.+||..||..-+    +..+++|-++..+
T Consensus        13 VS~a-TVSrvLn~~-~~Vs~eTr~rV~~aa~eLgY~Pn~~Ar~L~~~~s~~Igvv~~~~   69 (346)
T PRK10401         13 VSVA-TVSRVLNNS-ALVSPDTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDV   69 (346)
T ss_pred             CCHH-HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEECCC
T ss_conf             7999-999997794-99999999999999999499848888865007788799994788


No 260
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.96  E-value=32  Score=12.03  Aligned_cols=47  Identities=13%  Similarity=0.172  Sum_probs=29.0

Q ss_pred             CCCCCHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             52369999999998789------999888799999989999999998875304
Q gi|254780182|r  446 TMYLSEVQTRAILELRL------ARLTGLGRDDIRNELNSLGIEIKECLDILS  492 (910)
Q Consensus       446 ~f~lSe~QA~AILdMrL------~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~  492 (910)
                      .++||-.+...||+++=      ......=..-+.+...++.++|++|+..+.
T Consensus        53 ~lgfsL~eIk~ll~l~~~~~~~~~~~~~~v~~~l~~k~~eie~ki~eLq~~~~  105 (107)
T cd04777          53 GLGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKKAIQ  105 (107)
T ss_pred             HCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88998999999996243557674888999999999999999999999999996


No 261
>cd04803 CBS_pair_15 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=24.94  E-value=31  Score=12.16  Aligned_cols=32  Identities=19%  Similarity=0.304  Sum_probs=19.9

Q ss_pred             CHHHHHHHHHHHCCCHHCCCCCCCCCCCC-CCC
Q ss_conf             04789999997122011156131478870-887
Q gi|254780182|r   89 GNAAIYDALARMAQDWSLRLLLIEGQGNF-GSV  120 (910)
Q Consensus        89 Gd~siy~a~v~maq~~~~r~plidg~Gnf-Gs~  120 (910)
                      -|++++||+-.|.+.--.+.|.+|..|.+ |-+
T Consensus         8 ~~~tl~~a~~~m~~~~i~~lpVvd~~~~lvGii   40 (122)
T cd04803           8 EDDSLADAEELMREHRIRHLPVVNEDGKLVGLL   40 (122)
T ss_pred             CCCCHHHHHHHHHHCCCCEEEEECCCCCEEEEE
T ss_conf             969999999999974997899990898688896


No 262
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=24.69  E-value=22  Score=13.61  Aligned_cols=61  Identities=30%  Similarity=0.443  Sum_probs=39.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHC--------CCHHCC------CC
Q ss_conf             4000897367899999998789999981134042556643668870478999999712--------201115------61
Q gi|254780182|r   44 DLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMA--------QDWSLR------LL  109 (910)
Q Consensus        44 d~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~ma--------q~~~~r------~p  109 (910)
                      .|-+||-||+||  =+||-.|-..++|+    ..+-||+       |-|+=||+.--|        ||-|..      =.
T Consensus        10 ~VL~gLEPVr~R--PGMY~GGtD~~~~~----HL~~EV~-------DN~~DEA~AGfA~~i~v~lH~D~Si~v~D~GRG~   76 (647)
T TIGR01055        10 EVLDGLEPVRKR--PGMYTGGTDTTRPN----HLVQEVI-------DNSVDEALAGFASKIEVILHQDQSIEVIDNGRGM   76 (647)
T ss_pred             HHHCCCCCCCCC--CCCEECCCCCCCCH----HHHHHHH-------HHHHHHHHCCCCEEEEEEECCCCEEEEEECCCCC
T ss_conf             220168773428--87201786565301----3455544-------3335555406530788998289617998888303


Q ss_pred             CCCCCCCC
Q ss_conf             31478870
Q gi|254780182|r  110 LIEGQGNF  117 (910)
Q Consensus       110 lidg~Gnf  117 (910)
                      =||-|-.|
T Consensus        77 PvD~HP~~   84 (647)
T TIGR01055        77 PVDIHPKE   84 (647)
T ss_pred             CCCCCCCC
T ss_conf             44278888


No 263
>pfam05889 SLA_LP_auto_ag Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). This family consists of several eukaryotic and archaeal proteins which are related to the human soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis. The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway. Some archaeal members are annotated as being pyridoxal phosphate-dependent enzymes.
Probab=24.67  E-value=33  Score=11.99  Aligned_cols=32  Identities=13%  Similarity=0.393  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99998875304989999999998999998405
Q gi|254780182|r  482 IEIKECLDILSSRSRLLGIIKQELLSVKDELD  513 (910)
Q Consensus       482 ~~I~~l~~IL~s~~~l~~iI~~EL~eik~kyg  513 (910)
                      -=.+.|+++|..+++....+.++|.++.++||
T Consensus       268 lG~~gy~~Ll~eRke~~~~l~e~L~~~a~~~g  299 (389)
T pfam05889       268 LGCKAYLALMKEQKEMFPLLRELLKDLAEEVG  299 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             74888999999999999999999999999829


No 264
>pfam05904 DUF863 Plant protein of unknown function (DUF863). This family consists of a number of hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=24.60  E-value=27  Score=12.67  Aligned_cols=12  Identities=17%  Similarity=0.473  Sum_probs=4.3

Q ss_pred             CCHHHHHHHHHH
Q ss_conf             699999999987
Q gi|254780182|r  449 LSEVQTRAILEL  460 (910)
Q Consensus       449 lSe~QA~AILdM  460 (910)
                      |-.+-|+||..|
T Consensus       522 l~~iAAEaIVaI  533 (730)
T pfam05904       522 LIKIAAESIVAI  533 (730)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999998


No 265
>KOG0240 consensus
Probab=24.57  E-value=33  Score=11.98  Aligned_cols=56  Identities=25%  Similarity=0.284  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             9999878999988------8799999989999999998875304989999999998999998
Q gi|254780182|r  455 RAILELRLARLTG------LGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKD  510 (910)
Q Consensus       455 ~AILdMrL~rLt~------LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~  510 (910)
                      ..++.=++.+|-.      .+.++..+...+|..+..+=+.++++..++...+..|+.++.+
T Consensus       416 ~~~~~e~~~~L~qqlD~kd~~~n~~sqL~~~lk~q~~~qee~~s~~~~~~e~~q~e~~~~Q~  477 (607)
T KOG0240         416 EDILTERIESLYQQLDQKDDQINKQSQLMEKLKEQLLDQEELLSSTRRLYEDIQQELSEIQE  477 (607)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999998877778888999999999999987776655568879999999999999


No 266
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=24.48  E-value=33  Score=11.96  Aligned_cols=39  Identities=18%  Similarity=0.258  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             06999999861899789878776312697889999974022111222344523699999999987899
Q gi|254780182|r  396 NLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLA  463 (910)
Q Consensus       396 nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~  463 (910)
                      .|++||++-=....+=||....                             |+|||.|+..|.--.|.
T Consensus         1 di~riIemAweDrt~Fe~I~~~-----------------------------~gl~E~evi~lMr~~Lk   39 (72)
T TIGR03643         1 DIDRIIEMAWEDRTPFEAIEQQ-----------------------------FGLSEKEVIKLMRQNLK   39 (72)
T ss_pred             CHHHHHHHHHCCCCCHHHHHHH-----------------------------HCCCHHHHHHHHHHHCC
T ss_conf             9889999998379989999999-----------------------------89499999999996338


No 267
>TIGR02817 adh_fam_1 zinc-binding alcohol dehydrogenase family protein; InterPro: IPR014182   Members of this entry form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases. Some current members of this entry carry designations as putative alginate lyase, however none have been characterised as such..
Probab=24.43  E-value=20  Score=13.95  Aligned_cols=12  Identities=42%  Similarity=0.800  Sum_probs=6.6

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             7887088776972
Q gi|254780182|r  113 GQGNFGSVDGDPP  125 (910)
Q Consensus       113 g~GnfGs~dgd~~  125 (910)
                      +||-||=|| ||+
T Consensus       241 PQGrlaLID-DP~  252 (338)
T TIGR02817       241 PQGRLALID-DPA  252 (338)
T ss_pred             CCCCEECCC-CCC
T ss_conf             787400002-870


No 268
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA; InterPro: IPR010222   This entry represents HrpA, one of two related but uncharacterised DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterised, is about 800 amino acids long. Related characterised eukaryotic proteins are RNA helicases associated with pre-mRNA processing.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity.
Probab=24.24  E-value=33  Score=11.93  Aligned_cols=27  Identities=15%  Similarity=0.091  Sum_probs=13.1

Q ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999---99999999999999888778
Q gi|254780182|r  360 AFVAFRE---EVVVRRTKYLLNKARDRAHV  386 (910)
Q Consensus       360 ~fi~hR~---evi~rRt~~~L~ka~~R~HI  386 (910)
                      .+.++.-   |-++....|+--+++.|.|+
T Consensus      1139 l~~e~~g~lPe~VR~~a~F~al~~~vR~~l 1168 (1320)
T TIGR01967      1139 LIFENGGVLPEQVRTEAEFAALLEKVRAEL 1168 (1320)
T ss_pred             HHHHCCCCCCCCCCCHHHHHHHHHHHCHHH
T ss_conf             987268869877889899999997407324


No 269
>PRK09413 insertion sequence 2 OrfA protein; Reviewed
Probab=24.23  E-value=33  Score=11.93  Aligned_cols=38  Identities=18%  Similarity=0.196  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99899999999988753049899999999989999984
Q gi|254780182|r  474 RNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDE  511 (910)
Q Consensus       474 ~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~k  511 (910)
                      ..|.+.++++|.+|+.+|+....-.+++++-+.--+.|
T Consensus        70 ase~~~~~k~ireLqR~LGkktle~EILkeAve~~r~k  107 (121)
T PRK09413         70 ASELAAAMKQIKELQRLLGKKTMENELLKEAVEYGRAK  107 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH
T ss_conf             79999999889999999665489999999999987665


No 270
>cd04612 CBS_pair_SpoIVFB_EriC_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC.  SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus).  SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB.  It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase an
Probab=24.21  E-value=30  Score=12.36  Aligned_cols=10  Identities=60%  Similarity=0.790  Sum_probs=3.2

Q ss_pred             HHHHHHHHHC
Q ss_conf             8999999712
Q gi|254780182|r   92 AIYDALARMA  101 (910)
Q Consensus        92 siy~a~v~ma  101 (910)
                      ++++++-.|.
T Consensus        74 ~l~~a~~~m~   83 (111)
T cd04612          74 TLRDALKRMA   83 (111)
T ss_pred             CHHHHHHHHH
T ss_conf             7999999999


No 271
>TIGR00345 arsA arsenite-activated ATPase (arsA); InterPro: IPR003348   This ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.    In Escherichia coli an anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773. This ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance .   The ArsA and ArsB proteins form a membrane-bound pump that functions as an oxyanion-translocating ATPase. The ArsC protein is an arsenate reductase that reduces arsenate to arsenite, which is subsequently pumped out of the cell .; GO: 0005524 ATP binding, 0006820 anion transport, 0016020 membrane.
Probab=24.18  E-value=33  Score=11.92  Aligned_cols=29  Identities=28%  Similarity=0.420  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHH
Q ss_conf             87999999899999999988753049899
Q gi|254780182|r  468 LGRDDIRNELNSLGIEIKECLDILSSRSR  496 (910)
Q Consensus       468 LE~~kl~~E~~eL~~~I~~l~~IL~s~~~  496 (910)
                      |+.+++-++.+++.++|+.+.++|.|+++
T Consensus       199 l~~~~~l~~~~e~Ke~~~~~~~~l~DP~~  227 (330)
T TIGR00345       199 LEDDEALEKLEELKEQIEAAREVLSDPER  227 (330)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             87789999899999999999997249985


No 272
>cd04619 CBS_pair_6 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=24.13  E-value=33  Score=11.91  Aligned_cols=25  Identities=12%  Similarity=0.106  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHCCCHHCCCCCCCCC
Q ss_conf             4789999997122011156131478
Q gi|254780182|r   90 NAAIYDALARMAQDWSLRLLLIEGQ  114 (910)
Q Consensus        90 d~siy~a~v~maq~~~~r~plidg~  114 (910)
                      |.++++|+-.|.+.---+.|.+|..
T Consensus        75 ~~~i~~a~~~M~~~~i~~lPVVD~~   99 (114)
T cd04619          75 GDLLHDVWQVMKQRGLKNIPVVDEN   99 (114)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEEECC
T ss_conf             8909999998887698588999079


No 273
>TIGR02742 TrbC_Ftype type-F conjugative transfer system pilin assembly protein TrbC; InterPro: IPR014113   This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA , . The N-terminal portion of these proteins is heterogeneous. .
Probab=24.12  E-value=28  Score=12.63  Aligned_cols=14  Identities=50%  Similarity=0.736  Sum_probs=5.3

Q ss_pred             CHHHHHHHHHHHCC
Q ss_conf             04789999997122
Q gi|254780182|r   89 GNAAIYDALARMAQ  102 (910)
Q Consensus        89 Gd~siy~a~v~maq  102 (910)
                      ||-|||.||=.|+|
T Consensus       107 Gn~Sl~~ALe~~~~  120 (139)
T TIGR02742       107 GNVSLKGALEKMAQ  120 (139)
T ss_pred             EEEEHHHHHHHHHH
T ss_conf             30015778999874


No 274
>PRK04885 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=24.11  E-value=33  Score=11.91  Aligned_cols=46  Identities=15%  Similarity=0.180  Sum_probs=27.5

Q ss_pred             HHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEECCCEECC
Q ss_conf             3049899999999989999984056883310013434530101456781899907970523
Q gi|254780182|r  490 ILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSHLGYVKR  550 (910)
Q Consensus       490 IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~GyIKr  550 (910)
                      |.+++...-..+++.+++.-+++|-..           +.    ++-+++|++=-+|.+=+
T Consensus         5 iv~~~~~~s~~~~~~~~~~l~~~~~~~-----------~~----~~~Dlvi~iGGDGT~L~   50 (265)
T PRK04885          5 IISNGDEKSKRVASKLKKYLKDFGFIL-----------DE----KNPDIVISVGGDGTLLS   50 (265)
T ss_pred             EEECCCHHHHHHHHHHHHHHHHCCCCC-----------CC----CCCCEEEEECCCHHHHH
T ss_conf             996969899999999999998769855-----------87----78999999887399999


No 275
>TIGR01334 modD modD protein; InterPro: IPR006242   The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). Their function is unknown. ; GO: 0016763 transferase activity transferring pentosyl groups.
Probab=24.09  E-value=33  Score=11.91  Aligned_cols=75  Identities=20%  Similarity=0.202  Sum_probs=54.6

Q ss_pred             ECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf             41663000299999999999999999999999999988877--------8999999874069999998618997898787
Q gi|254780182|r  345 NGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAH--------VLVGLAIAVANLDEVVRIIRFSPNPETARRE  416 (910)
Q Consensus       345 ~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~H--------ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~  416 (910)
                      -+|.=...||-|-|=-|-+||.=.-   -.+|..++=.|+.        .||     .+++.+.+.+.|.+.|.=    .
T Consensus       146 aGG~iHR~glsETlLvFanHr~fl~---D~~Dw~gai~rLkq~APE~KItvE-----adt~~qa~~~l~a~PDil----Q  213 (277)
T TIGR01334       146 AGGLIHRAGLSETLLVFANHRTFLS---DNEDWSGAITRLKQQAPEKKITVE-----ADTLKQALAVLRADPDIL----Q  213 (277)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHHCC---CCCHHHHHHHHHHHHCCCCCEEEE-----ECCHHHHHHHHHCCCCEE----E
T ss_conf             1605654115899999998786417---800278999887743787726874-----059899999974489766----3


Q ss_pred             HHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             76312697889999974022111222344523699999999987
Q gi|254780182|r  417 LMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILEL  460 (910)
Q Consensus       417 L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdM  460 (910)
                                                   .-+||..|+..|+++
T Consensus       214 -----------------------------LdKFtpqQ~~~~~~~  228 (277)
T TIGR01334       214 -----------------------------LDKFTPQQVKELLEL  228 (277)
T ss_pred             -----------------------------CCCCCHHHHHHHHHH
T ss_conf             -----------------------------236888899999999


No 276
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I; InterPro: IPR011775    This entry represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll . This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. It is also found in certain archaea not known to make chlorins.; GO: 0005524 ATP binding, 0016851 magnesium chelatase activity, 0006779 porphyrin biosynthetic process.
Probab=24.02  E-value=18  Score=14.35  Aligned_cols=143  Identities=23%  Similarity=0.333  Sum_probs=79.8

Q ss_pred             HCCCCCCHHHHHHHHHHHHHCC-CCCHHHHH-HHCCCCCCCCCCC---CCCHHHHHHHHHHCCCEEE--EEEEEEEEECC
Q ss_conf             1789854789999998876187-76888888-6345866887443---4475889999870120389--99988654336
Q gi|254780182|r  188 TNIPTHNLGEVVDGCVAVIDNP-DIDLDALM-EIIRGPDFPTGAV---ILGRTGIKNAYATGRGSIV--IRGVSHIEKTS  260 (910)
Q Consensus       188 TnippHNl~Ev~~a~~~~i~~p-~~~~~eL~-~~i~GPDFPTGG~---I~~~~~i~~~y~tGrG~i~--iR~k~~ie~~~  260 (910)
                      -|-.|-.-.+.|+-+.++-+.. +..--.++ +-+|==|.|-|..   +.|.=.|..|...|--.|-  +-||+      
T Consensus        60 ~n~~Ps~~~~~c~e~r~~~~~~Gkt~~~~~i~~pvpvVDLPLGaTEDRVcGtlDIerALt~GvkAFePGLLArA------  133 (340)
T TIGR02030        60 FNSAPSDREELCEEVRILEDSSGKTKKLAVIEKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARA------  133 (340)
T ss_pred             CCCCCCCCCCCCHHHHHHHHCCCCCCCCEEEECCCCEEECCCCCCCCCEECHHHHHHHHHCCCCCCCCCCHHHH------
T ss_conf             78888886135767777531268656751551576536479886213134402476775047210366304666------


Q ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHH----CCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCC
Q ss_conf             784599992464435289999999999871665014458730----3746557999947988778999999976101100
Q gi|254780182|r  261 GDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDE----SDRQGYRVVIELKRGASADVILNQLYRYTSLQSL  336 (910)
Q Consensus       261 ~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDe----Sdr~giRivielKr~~~~~~vln~Lyk~T~Lq~s  336 (910)
                       +|=-+.|-|.       +|+|       +.-++-+-|+.--    =-|+|+.|=                         
T Consensus       134 -NRG~LYiDEV-------NLLe-------DHlVDvLLDvAasG~NvVEREG~SiR-------------------------  173 (340)
T TIGR02030       134 -NRGYLYIDEV-------NLLE-------DHLVDVLLDVAASGVNVVEREGVSIR-------------------------  173 (340)
T ss_pred             -CCCCEEEEEE-------HHHH-------HHHHHHHHHHCCCCCEEEEECCEEEE-------------------------
T ss_conf             -1784255210-------0012-------45665665220478305863560230-------------------------


Q ss_pred             CCCEEEEEE-CCCCCCCCHH-HHHHHH-----------HHHHHHHHHHHHHHHH
Q ss_conf             000024554-1663000299-999999-----------9999999999999999
Q gi|254780182|r  337 FSVNMVALN-GYKPERFTLI-GILKAF-----------VAFREEVVVRRTKYLL  377 (910)
Q Consensus       337 f~~N~~aL~-~g~P~~l~Lk-~iL~~f-----------i~hR~evi~rRt~~~L  377 (910)
                      -+.=|+ || -|-|.-=.|+ |+|+.|           ++.|.+||+||++||-
T Consensus       174 HPARFV-LVGSGNPEEGeLRPQLLDRFGlhaeirt~rdve~RVeiv~rR~eyDa  226 (340)
T TIGR02030       174 HPARFV-LVGSGNPEEGELRPQLLDRFGLHAEIRTVRDVEERVEIVKRRDEYDA  226 (340)
T ss_pred             CCCCEE-EECCCCCCCCCCCCHHHHHCCCEEEEECCCCHHHHHHHEEEHHHHCC
T ss_conf             376358-71578887666674015244652787226772220122010033177


No 277
>KOG3011 consensus
Probab=23.93  E-value=34  Score=11.88  Aligned_cols=37  Identities=32%  Similarity=0.497  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCC-EECCCCCCCCCEE
Q ss_conf             5789997899999986307684053-3068988548503
Q gi|254780182|r  129 RYTECRLQKAAHFLLDDLGKDTVDF-RPNYDGSFQEPVV  166 (910)
Q Consensus       129 RYte~rl~~~~~~~l~~i~~~tv~~-~~n~D~~~~EP~v  166 (910)
                      +.-+.-|+-+|..|++|+....|-| .+|| |+..-|.|
T Consensus       105 ~~~~~~La~~aG~i~AD~~SGl~HWaaD~~-Gsv~tP~v  142 (293)
T KOG3011         105 LWLEPALAAYAGYITADLGSGVYHWAADNY-GSVSTPWV  142 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCEEEEECCCC-CCCCCCHH
T ss_conf             637999999877998865145067521556-76544046


No 278
>COG0241 HisB Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]
Probab=23.73  E-value=21  Score=13.66  Aligned_cols=50  Identities=20%  Similarity=0.444  Sum_probs=18.8

Q ss_pred             CHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCC
Q ss_conf             11016761010133178985478999999887618776888888634586688744
Q gi|254780182|r  174 VLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGA  229 (910)
Q Consensus       174 lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG  229 (910)
                      +++---+|||.|+-|.   +++...-+.....+..-...++   .+.=+|.+|.++
T Consensus        51 VvvTNQsGi~rgyf~~---~~f~~~~~~m~~~l~~~gv~id---~i~~Cph~p~~~  100 (181)
T COG0241          51 VVVTNQSGIGRGYFTE---ADFDKLHNKMLKILASQGVKID---GILYCPHHPEDN  100 (181)
T ss_pred             EEEECCCCCCCCCCCH---HHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCCCC
T ss_conf             9998777755667668---9999899999999997497036---499878898777


No 279
>PRK08006 replicative DNA helicase; Provisional
Probab=23.69  E-value=34  Score=11.85  Aligned_cols=12  Identities=33%  Similarity=0.537  Sum_probs=5.1

Q ss_pred             HHHHHHCCCCCC
Q ss_conf             888863458668
Q gi|254780182|r  214 DALMEIIRGPDF  225 (910)
Q Consensus       214 ~eL~~~i~GPDF  225 (910)
                      +++..++..-||
T Consensus        49 ~~v~~~L~~edF   60 (471)
T PRK08006         49 DDVAERVVADDF   60 (471)
T ss_pred             HHHHHHCCHHHC
T ss_conf             999963698767


No 280
>pfam06530 Phage_antitermQ Phage antitermination protein Q. This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream.
Probab=23.62  E-value=34  Score=11.84  Aligned_cols=37  Identities=27%  Similarity=0.376  Sum_probs=19.6

Q ss_pred             CCEEEHHHHCCCCCC---------HHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             610101331789854---------7899999988761877688888
Q gi|254780182|r  180 GGIAVGMATNIPTHN---------LGEVVDGCVAVIDNPDIDLDAL  216 (910)
Q Consensus       180 ~GIAvGmaTnippHN---------l~Ev~~a~~~~i~~p~~~~~eL  216 (910)
                      +-||.|+...+|..+         -+-+||+|++.+...+...-+|
T Consensus        25 s~iaAgFk~lip~~~ksR~~CsDdDGliId~~va~L~~~~~~~~~l   70 (126)
T pfam06530        25 SPIAAGFKSLLPGRVKTRPMCSDDDGMIISQCVDSLMYIDPKLFGL   70 (126)
T ss_pred             HHHHHHHHCCCCCCCCCCCCEECCCCCHHHHHHHHHHHCCHHHHHH
T ss_conf             7899987135898899877330886332999999998739899999


No 281
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=23.58  E-value=34  Score=11.83  Aligned_cols=78  Identities=19%  Similarity=0.238  Sum_probs=37.2

Q ss_pred             CCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEE--EEEEEEEEECCC------CCEEEEEECCCCCCCHHH
Q ss_conf             877688888863458668874434475889999870120389--999886543367------845999924644352899
Q gi|254780182|r  208 NPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIV--IRGVSHIEKTSG------DREQIVVTEIPYQVNKAA  279 (910)
Q Consensus       208 ~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~--iR~k~~ie~~~~------~k~~ivItEiPY~vnk~~  279 (910)
                      ..++....|.++++|-||----++.=-..|+++-+.-.|-+.  +-|++-.++.+-      || ...|.|-|-    ++
T Consensus        38 ~anIP~StLYKil~G~dpr~~tl~~I~ktir~~ek~en~~fiA~IAAR~vL~~i~~~kk~i~gk-~~~ireYpa----~s  112 (170)
T COG4800          38 RANIPLSTLYKILKGSDPRYDTLTRIFKTIRSYEKKENIGFIALIAARYVLEEIKFGKKGINGK-SYLIREYPA----SS  112 (170)
T ss_pred             HCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHCCCCCC-EEEEEECCC----CC
T ss_conf             7099899999998179965778999999999887504778466534488998887601033673-368874364----52


Q ss_pred             HHHHHHHHHHC
Q ss_conf             99999999871
Q gi|254780182|r  280 MLEKIAELVRE  290 (910)
Q Consensus       280 lie~Ia~lv~~  290 (910)
                      |-|-|...|+.
T Consensus       113 lEeaIvAaVrA  123 (170)
T COG4800         113 LEEAIVAAVRA  123 (170)
T ss_pred             HHHHHHHHHHH
T ss_conf             89999999986


No 282
>PRK06819 flagellin; Validated
Probab=23.57  E-value=34  Score=11.83  Aligned_cols=22  Identities=27%  Similarity=0.338  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8887999999899999999988
Q gi|254780182|r  466 TGLGRDDIRNELNSLGIEIKEC  487 (910)
Q Consensus       466 t~LE~~kl~~E~~eL~~~I~~l  487 (910)
                      +.-||..|..|+++|..+|..+
T Consensus       104 s~~DR~~i~~Ei~ql~~ei~~i  125 (371)
T PRK06819        104 SASDLDSIQDEINQRLAEIDRV  125 (371)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7678999999999999999999


No 283
>PRK07263 consensus
Probab=23.53  E-value=34  Score=11.82  Aligned_cols=23  Identities=26%  Similarity=0.406  Sum_probs=16.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98999999999899999840568
Q gi|254780182|r  493 SRSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       493 s~~~l~~iI~~EL~eik~kygd~  515 (910)
                      ++......|-..|+.+.+.++-|
T Consensus       334 ~r~~ev~~isr~lK~lAkel~ip  356 (453)
T PRK07263        334 NRQQEVSDISRQLKILAKELKVP  356 (453)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             59999999999999999987997


No 284
>PRK08411 flagellin; Reviewed
Probab=23.44  E-value=34  Score=11.81  Aligned_cols=62  Identities=16%  Similarity=0.212  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             89999998740699999986189978987877631269788999997402211122234452369999999998789999
Q gi|254780182|r  386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL  465 (910)
Q Consensus       386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL  465 (910)
                      -+.||-.|..|.-.-|.+|..++      -.|-+                                  ...||. |+|.|
T Consensus        57 QI~GL~qA~rNanDgISl~QTAE------GAL~E----------------------------------v~~iLq-RmREL   95 (573)
T PRK08411         57 QANTLGQAISNGNDALGILQTAD------KAMDE----------------------------------QLKILD-TIKTK   95 (573)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH------HHHHH----------------------------------HHHHHH-HHHHH
T ss_conf             98889999986988999999999------99999----------------------------------999999-99999


Q ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------88879999998999999999887
Q gi|254780182|r  466 ---------TGLGRDDIRNELNSLGIEIKECL  488 (910)
Q Consensus       466 ---------t~LE~~kl~~E~~eL~~~I~~l~  488 (910)
                               +.-+|..|++|+++|.++|.++-
T Consensus        96 AVQAAN~tns~~DR~alQ~Ei~qL~~EIdRIa  127 (573)
T PRK08411         96 ATQAAQDGQSLKTRTMLQADINRLMEELDNIA  127 (573)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99961468998999999999999999997661


No 285
>TIGR00501 met_pdase_II methionine aminopeptidase, type II; InterPro: IPR002468   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to MEROPS peptidase family M24 (clan MG), subfamily M24A.   Methionine aminopeptidase (3.4.11.18 from EC) (MAP) is responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged. All MAP studied to date are monomeric proteins that require cobalt ions for activity. Two subfamilies of MAP enzymes are known to exist , . While being evolutionary related, they only share a limited amount of sequence similarity mostly clustered around the residues shown, in the Escherichia coli MAP , to be involved in cobalt-binding. The first family consists of enzymes from prokaryotes as well as eukaryotic MAP-1, while the second group (IPR002467 from INTERPRO) is made up of archaeal MAP and eukaryotic MAP-2 and includes proteins which do not seem to be MAP, but that are clearly evolutionary related such as mouse proliferation-associated protein 1 and fission yeast curved DNA-binding protein. ; GO: 0004239 methionyl aminopeptidase activity, 0006508 proteolysis.
Probab=23.42  E-value=16  Score=14.70  Aligned_cols=38  Identities=21%  Similarity=0.225  Sum_probs=25.8

Q ss_pred             EEECCCCEE-EEEEECCCCCEEEEEECCCEEEEEEHHHC-CCC
Q ss_conf             661589857-88896189826999936985999758762-354
Q gi|254780182|r  676 MKLDSRDEI-LSVETCTQENDILLTTKLGQCVRFPISAI-RVF  716 (910)
Q Consensus       676 ikLkegD~L-i~v~~~~~~~~Iil~T~~G~~lrF~~~ev-r~~  716 (910)
                      -+|.+||-+ |-.|-+   +=+-+||..|.+-.|....- ||+
T Consensus       205 ~~leeG~~~AIEpFAt---~G~G~V~~~~~~~iY~~l~~Drpv  244 (327)
T TIGR00501       205 TKLEEGDVVAIEPFAT---DGVGLVTDGGEVEIYKFLAEDRPV  244 (327)
T ss_pred             CEEECCCEEEECCCCC---CCEEEEECCCCCHHHHHHCCCCCC
T ss_conf             4510257888436676---874565128861012210568896


No 286
>PHA02094 hypothetical protein
Probab=23.17  E-value=35  Score=11.77  Aligned_cols=20  Identities=30%  Similarity=0.620  Sum_probs=14.2

Q ss_pred             EEEEHHHHHHHHCCCCCCCH
Q ss_conf             11340425566436688704
Q gi|254780182|r   71 YVKCARISGEVMGKYHPHGN   90 (910)
Q Consensus        71 ~~K~a~ivg~v~gkyHPHGd   90 (910)
                      |---|+-||+.+|..||..-
T Consensus        43 ye~~~ksig~m~g~~hptak   62 (81)
T PHA02094         43 YEFFAKSVGAMIGELHPTAK   62 (81)
T ss_pred             HHHHHHHHHHHHCCCCCCCC
T ss_conf             99999999999623586301


No 287
>TIGR00444 mazG MazG family protein; InterPro: IPR011551   This group of prokaryotic proteins has no known function. It includes the uncharacterised protein MazG in Escherichia coli..
Probab=23.07  E-value=20  Score=13.84  Aligned_cols=15  Identities=27%  Similarity=0.521  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999998999999999
Q gi|254780182|r  471 DDIRNELNSLGIEIK  485 (910)
Q Consensus       471 ~kl~~E~~eL~~~I~  485 (910)
                      +|+.+|++|...++.
T Consensus       163 ~Kv~EEl~E~~~e~~  177 (253)
T TIGR00444       163 DKVSEELEEVKSEVS  177 (253)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             877888899999985


No 288
>PRK13588 flagellin B; Provisional
Probab=23.06  E-value=35  Score=11.75  Aligned_cols=63  Identities=16%  Similarity=0.255  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             89999998740699999986189978987877631269788999997402211122234452369999999998789999
Q gi|254780182|r  386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL  465 (910)
Q Consensus       386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL  465 (910)
                      -+.||-.|..|.-.=|.+++-++      -.|-+                                .  ..||. |+|.|
T Consensus        57 Qi~gl~qA~rNa~dgiSliQTAE------GAL~E--------------------------------v--~~iLq-RmREL   95 (514)
T PRK13588         57 QAANLGQAIRNANDAIGIVQTAD------KAMDE--------------------------------Q--IKILD-TIKTK   95 (514)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH------HHHHH--------------------------------H--HHHHH-HHHHH
T ss_conf             99889999986888999999999------99999--------------------------------9--99999-99999


Q ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------888799999989999999998875
Q gi|254780182|r  466 ---------TGLGRDDIRNELNSLGIEIKECLD  489 (910)
Q Consensus       466 ---------t~LE~~kl~~E~~eL~~~I~~l~~  489 (910)
                               +.-++..|++|+++|..+|.++-.
T Consensus        96 AVQAAN~t~s~~dR~alQ~Ei~qL~~EIdrIa~  128 (514)
T PRK13588         96 AVQAAQDGQTLESRRALQSDIQRLLEELDNIAN  128 (514)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998703789888999999999999999987765


No 289
>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=23.04  E-value=35  Score=11.75  Aligned_cols=17  Identities=24%  Similarity=0.405  Sum_probs=8.4

Q ss_pred             EEECCCCEEEEEEECCC
Q ss_conf             66158985788896189
Q gi|254780182|r  676 MKLDSRDEILSVETCTQ  692 (910)
Q Consensus       676 ikLkegD~Li~v~~~~~  692 (910)
                      |+|.+||-+++.--+++
T Consensus       120 mnL~EgDPViSmGDt~G  136 (230)
T pfam12226       120 LNLAEGDPVISMGDTTG  136 (230)
T ss_pred             HCCCCCCCEEEECCCCC
T ss_conf             33336996565136778


No 290
>PRK11462 putative transporter; Provisional
Probab=23.02  E-value=35  Score=11.75  Aligned_cols=28  Identities=21%  Similarity=0.145  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9998789999888799999989999999
Q gi|254780182|r  456 AILELRLARLTGLGRDDIRNELNSLGIE  483 (910)
Q Consensus       456 AILdMrL~rLt~LE~~kl~~E~~eL~~~  483 (910)
                      +++-||-|+||+-...+|++|+++-+++
T Consensus       421 ~ii~~~~Y~L~~~~~~eI~~eL~~~~~~  448 (460)
T PRK11462        421 AIIAKRYYSLTTHNLKTVMEQLAQGKRR  448 (460)
T ss_pred             HHHHHHEECCCHHHHHHHHHHHHHHHHH
T ss_conf             9999952359899999999999999884


No 291
>cd04631 CBS_pair_18 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=22.96  E-value=34  Score=11.90  Aligned_cols=28  Identities=21%  Similarity=0.335  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHCCCHHCCCCCCCC-CCCC
Q ss_conf             478999999712201115613147-8870
Q gi|254780182|r   90 NAAIYDALARMAQDWSLRLLLIEG-QGNF  117 (910)
Q Consensus        90 d~siy~a~v~maq~~~~r~plidg-~Gnf  117 (910)
                      |+++++|+-.|.+.--.+.|.+|- +|.+
T Consensus         9 ~~tl~ea~~~m~~~~v~~~PVvd~~~~~l   37 (125)
T cd04631           9 TTPIMEAAKIMVRNGFRRLPVVDEGTGKL   37 (125)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEEECCCCCE
T ss_conf             09499999999983998899997999959


No 292
>KOG4777 consensus
Probab=22.89  E-value=35  Score=11.73  Aligned_cols=111  Identities=28%  Similarity=0.331  Sum_probs=51.0

Q ss_pred             CCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHH--HHHHHHHH--------------H---HHHH
Q ss_conf             668870478999999712201115613147887088776972013578--99978999--------------9---9986
Q gi|254780182|r   84 KYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYT--ECRLQKAA--------------H---FLLD  144 (910)
Q Consensus        84 kyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYt--e~rl~~~~--------------~---~~l~  144 (910)
                      .-|||-.-.+-.|--|-|-   .||..   -|||---|--|-.|--||  ||.-..|.              .   .++.
T Consensus        25 sdhP~f~ikvLgAS~RSAG---K~ya~---a~~wkqt~~lp~~~~e~~V~ec~~~~F~ecDIvfsgldad~ageiek~f~   98 (361)
T KOG4777          25 SDHPYFSIKVLGASKRSAG---KRYAF---AGNWKQTDLLPESAHEYTVEECTADSFNECDIVFSGLDADIAGEIEKLFA   98 (361)
T ss_pred             CCCCCCEEEEECCCCCCCC---CCEEE---CCCCHHCCCCCCHHHHHHHHHCCHHHCCCCCEEEECCCCHHHHHHHHHHH
T ss_conf             1698513423013331469---81576---04411202465034341375558402366558985278236656547788


Q ss_pred             HCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCH
Q ss_conf             307684053306898854850343227321101676101013317898547899999988761877688
Q gi|254780182|r  145 DLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDL  213 (910)
Q Consensus       145 ~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~  213 (910)
                      +-.--.|+-.-||--...-|.|.|.-=|--    -.||++|.-|+-|-.-         ++|-|++|++
T Consensus        99 eag~iiVsNaknyRre~~VPLvvP~VNpeh----ld~ik~~~~~~k~~~G---------~iI~nsNCST  154 (361)
T KOG4777          99 EAGTIIVSNAKNYRREDGVPLVVPEVNPEH----LDGIKVGLDTGKMGKG---------AIIANSNCST  154 (361)
T ss_pred             HCCEEEEECCHHCCCCCCCCEEECCCCHHH----HHHHEECCCCCCCCCC---------EEEECCCCCE
T ss_conf             668699867143025799745733458778----4253022225888995---------2896698870


No 293
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=22.72  E-value=35  Score=11.70  Aligned_cols=59  Identities=5%  Similarity=0.004  Sum_probs=31.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf             5236999999999878999988879999998999999999887530498999999999899999
Q gi|254780182|r  446 TMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVK  509 (910)
Q Consensus       446 ~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik  509 (910)
                      .-.|++.-+++-|.-+=..+..||     +.+++|.++++.+..=..+.++.++.+..+..++.
T Consensus        59 ~~~Ft~k~~qsAlt~qQ~~~~~le-----k~l~~l~~~l~~~~~~~~~~q~~l~~l~~~~~~l~  117 (474)
T PRK13729         59 DTTFDDKVRQHATTEMQVTAAQMQ-----KQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALA  117 (474)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             753436778879999999999999-----99999999999998765628999999999999999


No 294
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=22.72  E-value=21  Score=13.72  Aligned_cols=36  Identities=25%  Similarity=0.272  Sum_probs=20.4

Q ss_pred             HHCC-CCCEEEEEEECCCC-C-HHHHHHHHHHHCCHHCCC
Q ss_conf             3037-46557999947988-7-789999999761011000
Q gi|254780182|r  301 DESD-RQGYRVVIELKRGA-S-ADVILNQLYRYTSLQSLF  337 (910)
Q Consensus       301 DeSd-r~giRivielKr~~-~-~~~vln~Lyk~T~Lq~sf  337 (910)
                      |..+ ..|+||-++++-+. . -+.|..+| ++|.+-+-+
T Consensus       165 ~~~~~~hGt~Ve~~ieg~~~~~r~~v~eYl-r~TaIvnPh  203 (533)
T PRK04184        165 DNWKRWHGTRVELELEGNWYRAKQGIYEYL-KRTAIVNPH  203 (533)
T ss_pred             CCCCCCCCEEEEEEEEEEHHHHHCCHHHHH-HHHHCCCCC
T ss_conf             477788843999999764154423699999-765103784


No 295
>pfam04762 IKI3 IKI3 family. Members of this family are components of the elongator multi-subunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. This region contains WD40 like repeats.
Probab=22.59  E-value=35  Score=11.68  Aligned_cols=28  Identities=14%  Similarity=0.281  Sum_probs=10.7

Q ss_pred             CCCEEEEEEECCCCCEEEEEECCCEEEE
Q ss_conf             8985788896189826999936985999
Q gi|254780182|r  680 SRDEILSVETCTQENDILLTTKLGQCVR  707 (910)
Q Consensus       680 egD~Li~v~~~~~~~~Iil~T~~G~~lr  707 (910)
                      +.+.++.+....+.+.+++-+.+|+.+.
T Consensus       526 ~~~~~v~~~~~~~~~~~~~q~~~G~v~~  553 (918)
T pfam04762       526 ELDGIVLILSSNDYKHVFVQTRDGKVFS  553 (918)
T ss_pred             CCCCEEEEEEECCCCEEEEEECCCEEEE
T ss_conf             1686289994089856999957984999


No 296
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL; InterPro: IPR014285   NifL modulates the activity of the nitrogen fixation positive regulator protein NifA, acting as a negative regulator by binding NifA. NifA and NifL are encoded by adjacent genes..
Probab=22.54  E-value=36  Score=11.67  Aligned_cols=10  Identities=30%  Similarity=0.146  Sum_probs=4.4

Q ss_pred             EEEEECCCCC
Q ss_conf             9998200043
Q gi|254780182|r  598 VYKEKVWRLP  607 (910)
Q Consensus       598 vy~l~v~~IP  607 (910)
                      |=|.++..||
T Consensus       371 VdW~Pa~~LP  380 (496)
T TIGR02938       371 VDWQPAAVLP  380 (496)
T ss_pred             ECCCCCCCCC
T ss_conf             5165610162


No 297
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=22.52  E-value=36  Score=11.67  Aligned_cols=70  Identities=17%  Similarity=0.257  Sum_probs=48.6

Q ss_pred             CEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCC-------CC-------CCCHHHHHHHHH
Q ss_conf             8113404255664366887047899999971220111561314788708877-------69-------720135789997
Q gi|254780182|r   70 KYVKCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVD-------GD-------PPAAERYTECRL  135 (910)
Q Consensus        70 ~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs~d-------gd-------~~AA~RYte~rl  135 (910)
                      .|+...+....-.| +-|-|-|-..--=+-+.|.|++--|-=-|.--||.+.       |.       --.-++-|..||
T Consensus        67 e~e~~~~fF~k~~G-~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl  145 (1187)
T COG1110          67 EYEEFEEFFKKATG-FRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERL  145 (1187)
T ss_pred             HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHH
T ss_conf             99999999998638-98607889999998737844898278876547999999998755874999966789999999999


Q ss_pred             HHHHH
Q ss_conf             89999
Q gi|254780182|r  136 QKAAH  140 (910)
Q Consensus       136 ~~~~~  140 (910)
                      .++++
T Consensus       146 ~~~~e  150 (1187)
T COG1110         146 KKFAE  150 (1187)
T ss_pred             HHHHH
T ss_conf             99886


No 298
>PRK12756 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=22.50  E-value=36  Score=11.67  Aligned_cols=22  Identities=36%  Similarity=0.407  Sum_probs=9.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             877697201357899978999999
Q gi|254780182|r  119 SVDGDPPAAERYTECRLQKAAHFL  142 (910)
Q Consensus       119 s~dgd~~AA~RYte~rl~~~~~~~  142 (910)
                      ||+ ||.||+-|-+ ||.++++++
T Consensus        62 SIH-D~~aaleYA~-rL~~l~~~~   83 (349)
T PRK12756         62 SIH-DTDAALDYAT-RLQALREQY   83 (349)
T ss_pred             CCC-CHHHHHHHHH-HHHHHHHHH
T ss_conf             778-9799999999-999999972


No 299
>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional
Probab=22.50  E-value=36  Score=11.67  Aligned_cols=21  Identities=10%  Similarity=0.260  Sum_probs=9.4

Q ss_pred             CCCCCCCCC--HHHHHHHHHHHH
Q ss_conf             754000897--367899999998
Q gi|254780182|r   42 IPDLRDGLK--PVHRRILFGMMQ   62 (910)
Q Consensus        42 lPd~rDGlK--pv~Rrily~m~~   62 (910)
                      |...-.|+.  |-|+...-+.++
T Consensus        17 l~~~~~gfe~R~~Q~~Ma~~V~~   39 (697)
T PRK11747         17 LQEQLPGFIPRAGQRQMIAEVAK   39 (697)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             99868899718789999999999


No 300
>KOG3347 consensus
Probab=22.46  E-value=36  Score=11.66  Aligned_cols=37  Identities=35%  Similarity=0.457  Sum_probs=16.1

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             599992464435289999999999871665014458730
Q gi|254780182|r  264 EQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDE  302 (910)
Q Consensus       264 ~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDe  302 (910)
                      ..|+||--| ++.|+.+-++||+...=+-|. |+|+.-|
T Consensus         8 PNILvtGTP-G~GKstl~~~lae~~~~~~i~-isd~vkE   44 (176)
T KOG3347           8 PNILVTGTP-GTGKSTLAERLAEKTGLEYIE-ISDLVKE   44 (176)
T ss_pred             CCEEEECCC-CCCCHHHHHHHHHHHCCCEEE-HHHHHHH
T ss_conf             887986799-988025999999973985674-5567766


No 301
>TIGR01916 F420_puta_dedox F420-dependent oxidoreductase, putative; InterPro: IPR008225 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function..
Probab=22.43  E-value=32  Score=12.13  Aligned_cols=120  Identities=16%  Similarity=0.289  Sum_probs=56.3

Q ss_pred             CCCEEEE-------ECCCCCCCCC------CCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEEC
Q ss_conf             8939998-------2000432244------45655412454536556200256630125666871799994799189842
Q gi|254780182|r  595 LGFVYKE-------KVWRLPIGSP------QARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNK  661 (910)
Q Consensus       595 ~Gkvy~l-------~v~~IP~~sr------~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~  661 (910)
                      -|++..+       .|.+|  ..|      +.|--.+.+.+ +.+-++|+..          ...||+-=|+.|+|-=..
T Consensus        51 EG~~~~l~ei~Ps~~A~ei--A~RladvtGtGKDp~~~~ai-l~Ea~ev~~~----------~~~F~itetr~G~VcaNA  117 (260)
T TIGR01916        51 EGRIISLEEITPSPEAKEI--AARLADVTGTGKDPRFVQAI-LEEAEEVVRV----------GKPFLITETRHGLVCANA  117 (260)
T ss_pred             CCCCCCCCCCCCCHHHHHH--HHHHHHCCCCCCCHHHHHHH-HHHCCEEEEE----------CCCEEEEEECCCCEEEEE
T ss_conf             6762324678788789999--99875305689868988987-7624066632----------797369832666367750


Q ss_pred             HHHHHHCCCCCEEEEEECCCCEEEEEEEC-------CCCCE-EEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCC
Q ss_conf             36862047772278661589857888961-------89826-99993698599975876235478665535767528998
Q gi|254780182|r  662 LSDFIQINRSGKIAMKLDSRDEILSVETC-------TQEND-ILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGD  733 (910)
Q Consensus       662 l~ef~~~r~~G~~aikLkegD~Li~v~~~-------~~~~~-Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D  733 (910)
                      -=+=+|.-..-+..+-.+.+-   +|...       .+.+- |++.=.+|++.|--.-.+ +. |  +.||+.++=..|+
T Consensus       118 GvD~SN~~~G~~llLP~dPD~---SA~~ir~~L~el~G~~VgVIITDT~GRpFR~G~vGv-Ai-G--~aG~~~l~D~~G~  190 (260)
T TIGR01916       118 GVDESNVEEGELLLLPEDPDA---SAEKIRRGLRELLGKDVGVIITDTNGRPFREGQVGV-AI-G--AAGVKALKDWRGE  190 (260)
T ss_pred             CCCCCCCCCCEEECCCCCHHH---HHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCEE-EE-E--ECCCHHHHHCCCC
T ss_conf             557112478567358988378---999999999986398478999718888401687437-88-1--0040478732789


Q ss_pred             E
Q ss_conf             6
Q gi|254780182|r  734 Q  734 (910)
Q Consensus       734 ~  734 (910)
                      +
T Consensus       191 ~  191 (260)
T TIGR01916       191 K  191 (260)
T ss_pred             C
T ss_conf             5


No 302
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=22.28  E-value=36  Score=11.63  Aligned_cols=20  Identities=15%  Similarity=0.290  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             78999999874069999998
Q gi|254780182|r  385 HVLVGLAIAVANLDEVVRII  404 (910)
Q Consensus       385 HILeGL~~Al~nIDeVI~iI  404 (910)
                      ...+|...-.+++.++++-.
T Consensus        21 ~~~~Gh~~G~~~~~~i~~~~   40 (221)
T cd00475          21 DRIEGHKAGAEKLRDILRWC   40 (221)
T ss_pred             CHHHHHHHHHHHHHHHHHHH
T ss_conf             87899999999999999999


No 303
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA; InterPro: IPR014136   This entry represents the Ti-type conjugative transfer relaxase TraA. TraA contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, IPR005053 from INTERPRO) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, IPR014129 from INTERPRO). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer ..
Probab=22.24  E-value=36  Score=11.63  Aligned_cols=43  Identities=9%  Similarity=0.258  Sum_probs=21.9

Q ss_pred             CCCEEEEEECCCCEEEECHHHHHH-CCCCCEEEEEECCCCEEEE
Q ss_conf             871799994799189842368620-4777227866158985788
Q gi|254780182|r  644 NNLYVVFATKHGNVRRNKLSDFIQ-INRSGKIAMKLDSRDEILS  686 (910)
Q Consensus       644 ~~~~Lvl~Tk~G~VKkt~l~ef~~-~r~~G~~aikLkegD~Li~  686 (910)
                      .+..+|.+=.-|||---.+.-|.. ..+.|-++.-+-|.+.|-.
T Consensus       500 ~~~dvLviDEAGMV~S~Qm~r~l~~A~~AGaKvVLvGD~~QLqa  543 (888)
T TIGR02768       500 EDKDVLVIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQA  543 (888)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEECCHHHHCH
T ss_conf             47766898515441467788999999872760598488578244


No 304
>PRK10977 hypothetical protein; Provisional
Probab=22.21  E-value=36  Score=11.62  Aligned_cols=59  Identities=22%  Similarity=0.364  Sum_probs=47.3

Q ss_pred             HHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHH-HCCCCC
Q ss_conf             9998630768405330689885485034322732110167610101331789854789999998876-187768
Q gi|254780182|r  140 HFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVI-DNPDID  212 (910)
Q Consensus       140 ~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i-~~p~~~  212 (910)
                      +.++-|+-+...+|+|-|        |||- +.-.|-|||.=     --==||-+|-|.++++.-+- .=|.+|
T Consensus        48 ~g~iCDmfEGhAPyrPRY--------ilPD-Y~kfl~~Gs~f-----LeL~pp~dldeAln~L~IlYhHVPSvT  107 (510)
T PRK10977         48 EGVICDMFEGHAPYKPRY--------VLPD-YAKFLANGSEF-----LELEPAKDLDEALNLLTILYHHVPSVT  107 (510)
T ss_pred             CCCEECCCCCCCCCCCCC--------CCCC-HHHHHHCCCHH-----HCCCCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             292420457888898750--------0866-99999734354-----277982459999988999985188557


No 305
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=22.20  E-value=36  Score=11.62  Aligned_cols=90  Identities=20%  Similarity=0.402  Sum_probs=45.0

Q ss_pred             CCHHHHHHHH-HHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEE-EEE----EEE--EEEC---CC
Q ss_conf             5478999999-88761877688888863458668874434475889999870120389-999----886--5433---67
Q gi|254780182|r  193 HNLGEVVDGC-VAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIV-IRG----VSH--IEKT---SG  261 (910)
Q Consensus       193 HNl~Ev~~a~-~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~-iR~----k~~--ie~~---~~  261 (910)
                      +-..|.|+-+ -|++++.|-    .  .||.||||+-.-.+...|         |.-+ .+.    .|.  +|+.   =.
T Consensus       215 nGvSE~i~~am~Alln~GDe----V--LiP~P~YPlyta~v~L~G---------g~pV~y~~dEe~~w~PDiedLe~kIT  279 (518)
T PRK13355        215 NGVSELINLSMSALLDDGDE----V--LVPSPDYPLWTACVNLAG---------GTAVHYRCDEESEWYPDIDDIRSKIT  279 (518)
T ss_pred             CCHHHHHHHHHHHHCCCCCE----E--EECCCCCCCHHHHHHHCC---------CEEEEEEECCCCCCCCCHHHHHHHCC
T ss_conf             77679999999983689998----9--825999977899988609---------87889874522177889999985357


Q ss_pred             CCEEEEEECCCC---C-CCHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             845999924644---3-52899999999998716650144
Q gi|254780182|r  262 DREQIVVTEIPY---Q-VNKAAMLEKIAELVREKRIVDIA  297 (910)
Q Consensus       262 ~k~~ivItEiPY---~-vnk~~lie~Ia~lv~~~ki~gI~  297 (910)
                      .|++.+|--=|=   + |=....+++|+++.++..|--|+
T Consensus       280 ~kTKAIVInNPNNPTGAVyS~E~LeeIaeiArehdLiIIS  319 (518)
T PRK13355        280 SKTKAIVIINPNNPTGALYPKEVLQQIVDIAREHQLIIFS  319 (518)
T ss_pred             CCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHCCEEEEE
T ss_conf             1557999968989888788999999999999985969996


No 306
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=22.20  E-value=36  Score=11.62  Aligned_cols=43  Identities=16%  Similarity=0.203  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999989999999998875304989999999998999998405
Q gi|254780182|r  471 DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELD  513 (910)
Q Consensus       471 ~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kyg  513 (910)
                      ..++.|+.+++.+++.|+.=++--....+.+-.|...++++|.
T Consensus       159 eele~e~ee~~erlk~le~E~s~LeE~~~~l~~ev~~L~~r~~  201 (290)
T COG4026         159 EELEAEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDLKKRWD  201 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_conf             9999899999999999987898899999866218999999999


No 307
>CHL00191 ycf61 DNA-directed RNA polymerase subunit omega; Provisional
Probab=22.18  E-value=36  Score=11.62  Aligned_cols=17  Identities=35%  Similarity=0.524  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999988877
Q gi|254780182|r  369 VVRRTKYLLNKARDRAH  385 (910)
Q Consensus       369 i~rRt~~~L~ka~~R~H  385 (910)
                      |.+|++..++.+..|-.
T Consensus        11 i~~r~E~Li~aasNRY~   27 (74)
T CHL00191         11 ILYRSEELLNAASNRYK   27 (74)
T ss_pred             HHHHHHHHHHHHCCCEE
T ss_conf             99999999985135446


No 308
>PRK10869 recombination and repair protein; Provisional
Probab=22.15  E-value=36  Score=11.61  Aligned_cols=12  Identities=42%  Similarity=0.609  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             878999988879
Q gi|254780182|r  459 ELRLARLTGLGR  470 (910)
Q Consensus       459 dMrL~rLt~LE~  470 (910)
                      +-||..|.+|.+
T Consensus       302 e~RL~~i~~L~R  313 (553)
T PRK10869        302 EQRLSKQISLAR  313 (553)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999998


No 309
>pfam00534 Glycos_transf_1 Glycosyl transferases group 1. Mutations in this domain of subunit A of phosphatidylinositol N-acetylglucosaminyltransferase lead to disease (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharides. Members of this family transfer UDP, ADP, GDP or CMP linked sugars. The eukaryotic glycogen synthases may be distant members of this family.
Probab=22.14  E-value=36  Score=11.61  Aligned_cols=21  Identities=0%  Similarity=0.200  Sum_probs=11.5

Q ss_pred             CCCCCHHHHHHHHHHHHHCCC
Q ss_conf             898547899999988761877
Q gi|254780182|r  190 IPTHNLGEVVDGCVAVIDNPD  210 (910)
Q Consensus       190 ippHNl~Ev~~a~~~~i~~p~  210 (910)
                      ++|-|..++++++..+++||+
T Consensus       140 ~~~~~~~~l~~~i~~li~n~~  160 (172)
T pfam00534       140 VDPGDAEALAEAIEKLLKDEE  160 (172)
T ss_pred             ECCCCHHHHHHHHHHHHCCHH
T ss_conf             789999999999999987999


No 310
>pfam00768 Peptidase_S11 D-alanyl-D-alanine carboxypeptidase.
Probab=22.11  E-value=36  Score=11.61  Aligned_cols=84  Identities=19%  Similarity=0.246  Sum_probs=49.3

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             00089736789999999878999998113404255664366887047899999971220111561314788708877697
Q gi|254780182|r   45 LRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDP  124 (910)
Q Consensus        45 ~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~  124 (910)
                      ++.|-+.--|-.||+|.-          .||.=...+++.+...+...--+.|=.-|+.|.|..      =+|-+..|-+
T Consensus        84 l~~G~~~tv~dLl~~lll----------~S~NdAA~aLA~~v~Gs~~~Fv~~MN~~A~~LGm~~------T~F~np~GL~  147 (241)
T pfam00768        84 LKPGDKVTVRDLLRGLLV----------SSGNDAAVALAEKIAGSEKAFVKMMNAKAKQLGLKN------TRFVNPTGLD  147 (241)
T ss_pred             ECCCCEEEHHHHHHHHHH----------HCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC------CEEECCCCCC
T ss_conf             348999889999999987----------564599999999845829999999999999819999------8666687777


Q ss_pred             CCHHHHHHH-HHHHHHHHHHHH
Q ss_conf             201357899-978999999863
Q gi|254780182|r  125 PAAERYTEC-RLQKAAHFLLDD  145 (910)
Q Consensus       125 ~AA~RYte~-rl~~~~~~~l~~  145 (910)
                      ... -||-| -|+.++.+.+++
T Consensus       148 ~~~-~~sTA~Dla~l~~~~~~~  168 (241)
T pfam00768       148 NHG-QYSSARDLAILARALIKD  168 (241)
T ss_pred             CCC-CEECHHHHHHHHHHHHHH
T ss_conf             888-666799999999999874


No 311
>pfam07426 Dynactin_p22 Dynactin subunit p22. This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localizes to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis. Family members are approximately 170 residues long and seem to be restricted to mammals.
Probab=21.98  E-value=36  Score=11.59  Aligned_cols=19  Identities=16%  Similarity=0.118  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHCCHH
Q ss_conf             9999999998875304989
Q gi|254780182|r  477 LNSLGIEIKECLDILSSRS  495 (910)
Q Consensus       477 ~~eL~~~I~~l~~IL~s~~  495 (910)
                      ..++.++|+.|+.+|+|+.
T Consensus        97 ~~~~Le~i~~L~~vLds~~  115 (172)
T pfam07426        97 QAALLEQVHSLQPLLDSAH  115 (172)
T ss_pred             HHHHHHHHHHHHHHCCCHH
T ss_conf             9999999997451038298


No 312
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=21.90  E-value=36  Score=11.58  Aligned_cols=50  Identities=20%  Similarity=0.159  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCEEECC-CCC----CCCC-CCCCCCCEEEEEECCCEE
Q ss_conf             9999989999984056883310013-434----5301-014567818999079705
Q gi|254780182|r  499 GIIKQELLSVKDELDTPRRTRIVEG-LLD----MEDE-DCIVREDMVVTVSHLGYV  548 (910)
Q Consensus       499 ~iI~~EL~eik~kygd~RRT~I~~~-~~~----i~~E-dlI~~E~vvV~lS~~GyI  548 (910)
                      ..+.++|..+-++||-..=....+. +..    +..+ +-=.....+|.+-+.||.
T Consensus       121 em~~~~l~~~L~k~Gv~~i~~~Ge~FDP~~HeAv~~~~~~~~~~~tVv~v~qkGY~  176 (193)
T COG0576         121 EMTLDQLLDALEKLGVEEIGPEGEKFDPNLHEAVQRVESEDVEPNTVVEVLQKGYK  176 (193)
T ss_pred             HHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHEEEECCCCCCCCEEEEEEECCEE
T ss_conf             99999999999987987807889988978855103436789999948898505706


No 313
>TIGR03604 docking_ocin bacteriocin biosynthesis docking scaffold, SagD family. prokaryotic systems for making a general class of heterocycle-containing bacteriocins.
Probab=21.88  E-value=36  Score=11.57  Aligned_cols=54  Identities=19%  Similarity=0.317  Sum_probs=33.2

Q ss_pred             CCCCCEECCCCCCCCCEECCCCCCCCHHC-----------CCCCEEEHHHHCCCCCCHHHHHHHHHHHHHC
Q ss_conf             84053306898854850343227321101-----------6761010133178985478999999887618
Q gi|254780182|r  149 DTVDFRPNYDGSFQEPVVLCARYPNVLVN-----------GGGGIAVGMATNIPTHNLGEVVDGCVAVIDN  208 (910)
Q Consensus       149 ~tv~~~~n~D~~~~EP~vlP~~~P~lL~n-----------G~~GIAvGmaTnippHNl~Ev~~a~~~~i~~  208 (910)
                      ..++|++-+|=...+|+.+|+.+=.+...           .|+|.|.|-...      .-++.|++-+|+.
T Consensus        72 ~~i~W~~g~~L~~g~~v~VPa~~v~~~~~~~~~~~~~~~~~SnGlAaG~t~~------eA~~~gL~EviER  136 (377)
T TIGR03604        72 TPIGWVPGKSLTTGRPVLVPAQLVYYSYPEERGEDYIVPSTSTGLAAGETLE------EAILNGLLEVIER  136 (377)
T ss_pred             CEEECEECCCCCCCCEEEEEHHHHHCCCCCCCCCCCEECCCCCCCCCCCCHH------HHHHHHHHHHHHH
T ss_conf             8140548424578966785479964679877777714246787168889999------9999999999999


No 314
>KOG2896 consensus
Probab=21.86  E-value=37  Score=11.57  Aligned_cols=111  Identities=14%  Similarity=0.092  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCC
Q ss_conf             99999999999999999999999888778999999874069999998618997898787763126978899999740221
Q gi|254780182|r  358 LKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDS  437 (910)
Q Consensus       358 L~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~  437 (910)
                      |+--+---.++...|..++-.-       ++++..+-...-.+..+-+.-+...++|.+|.-+...      ...+..+ 
T Consensus        54 lqk~i~~~k~~~c~r~~~r~~~-------~~~~~~~q~~~~q~~~~~~~~~~v~~ek~rl~~~~i~------~~iL~~~-  119 (377)
T KOG2896          54 LQKSIRLKKDVECKRTELRVKI-------LERLHVEQCLSAQVQSMRVEMKEVSEEKLRLQIECIQ------LKILVLE-  119 (377)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHH-
T ss_conf             9999999998865588899886-------5678899999999999999888888999998999988------8899888-


Q ss_pred             CCCCCCCCCCCCCHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             11222344523699999999-----98789999888799999989999999998875304
Q gi|254780182|r  438 SYTIGSDGTMYLSEVQTRAI-----LELRLARLTGLGRDDIRNELNSLGIEIKECLDILS  492 (910)
Q Consensus       438 ~~~~~~~~~f~lSe~QA~AI-----LdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~  492 (910)
                                ..=..|-+||     ..+++++...--+..+.++..+|.++++.|.++.+
T Consensus       120 ----------~~l~~~~Ealsk~~~~~~k~~~kL~~kr~q~~~~q~~l~k~~k~l~e~~~  169 (377)
T KOG2896         120 ----------SNLQRQIEALSKKRAHLEKTKQKLEDKRQQFNASQVKLQKQLKSLIELRN  169 (377)
T ss_pred             ----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ----------89999999888899899999999999999987778888776999999999


No 315
>TIGR01034 metK S-adenosylmethionine synthetase; InterPro: IPR002133   S-adenosylmethionine synthetase (MAT, 2.5.1.6 from EC) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP . AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.   In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.   The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex, and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance .; GO: 0004478 methionine adenosyltransferase activity, 0005524 ATP binding, 0006730 one-carbon compound metabolic process.
Probab=21.77  E-value=30  Score=12.30  Aligned_cols=16  Identities=44%  Similarity=0.513  Sum_probs=9.2

Q ss_pred             HCCCCCEEEHHHHCCC
Q ss_conf             0167610101331789
Q gi|254780182|r  176 VNGGGGIAVGMATNIP  191 (910)
Q Consensus       176 ~nG~~GIAvGmaTnip  191 (910)
                      ==|=.||-+|||||=-
T Consensus       120 GAGDQGimFGYAt~ET  135 (393)
T TIGR01034       120 GAGDQGIMFGYATNET  135 (393)
T ss_pred             CCCCEEEEEEEECCCH
T ss_conf             8984057854422400


No 316
>PRK00927 tryptophanyl-tRNA synthetase; Reviewed
Probab=21.76  E-value=37  Score=11.55  Aligned_cols=115  Identities=16%  Similarity=0.170  Sum_probs=66.5

Q ss_pred             CCHHHHHHHHHH-HCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             877899999997-6101100000024554166300029999999999999999999999999998887789999998740
Q gi|254780182|r  318 ASADVILNQLYR-YTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVAN  396 (910)
Q Consensus       318 ~~~~~vln~Lyk-~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~n  396 (910)
                      .+++.|.+++-+ .|+-+......    ..++|...||-.|...|-+-                               .
T Consensus       208 d~~~~i~kKi~~a~TDs~~~i~~d----~~~rPev~NL~~I~s~fs~~-------------------------------~  252 (325)
T PRK00927        208 DDPKTIAKKIKKAVTDSERPIRYD----DPGKPEVSNLLTIYSAFTGK-------------------------------S  252 (325)
T ss_pred             CCHHHHHHHHHHCCCCCCCCCCCC----CCCCCCCCHHHHHHHHHCCC-------------------------------C
T ss_conf             899999999885757998775556----89998636499999984899-------------------------------8


Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             69999998618997898787763126978899999740221112223445236999999999878999988879999998
Q gi|254780182|r  397 LDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNE  476 (910)
Q Consensus       397 IDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E  476 (910)
                      ++++.+-.+ ...-.++|+.|.+                                    +|         .-+..-++++
T Consensus       253 ~eei~~~y~-g~g~g~~Kk~Lae------------------------------------~I---------i~~L~PIrek  286 (325)
T PRK00927        253 IEELEAEYE-GKGYGDFKKDLAE------------------------------------AV---------VEFLAPIQER  286 (325)
T ss_pred             HHHHHHHHC-CCCHHHHHHHHHH------------------------------------HH---------HHHHHHHHHH
T ss_conf             999999968-9988999999999------------------------------------99---------9996899999


Q ss_pred             HHHHHHHHHHHHHHHCCHHHHHHH-HHHHHHHHHHHCC
Q ss_conf             999999999887530498999999-9998999998405
Q gi|254780182|r  477 LNSLGIEIKECLDILSSRSRLLGI-IKQELLSVKDELD  513 (910)
Q Consensus       477 ~~eL~~~I~~l~~IL~s~~~l~~i-I~~EL~eik~kyg  513 (910)
                      +++|.+...++.+||.+-.+.-.. -.+=|.++++..|
T Consensus       287 ~~~L~~d~~~l~~IL~~Ga~KAr~iA~~tl~~Vr~~~G  324 (325)
T PRK00927        287 YEELLADPAYLDEILAEGAEKARAVASKTLKKVREAMG  324 (325)
T ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99998399999999999999999999999999998629


No 317
>COG2039 Pcp Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) [Posttranslational modification, protein turnover, chaperones]
Probab=21.71  E-value=37  Score=11.55  Aligned_cols=19  Identities=21%  Similarity=0.237  Sum_probs=11.7

Q ss_pred             CCCCCHHHHHHHHHHHHHC
Q ss_conf             8985478999999887618
Q gi|254780182|r  190 IPTHNLGEVVDGCVAVIDN  208 (910)
Q Consensus       190 ippHNl~Ev~~a~~~~i~~  208 (910)
                      +-|--+++..+++...|+.
T Consensus        40 ~lP~~f~~s~~~l~~~i~~   58 (207)
T COG2039          40 ILPVVFKKSIDALVQAIAE   58 (207)
T ss_pred             ECCCCHHHHHHHHHHHHHH
T ss_conf             8574188899999999985


No 318
>KOG4577 consensus
Probab=21.61  E-value=37  Score=11.53  Aligned_cols=54  Identities=19%  Similarity=0.119  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             899998887999999899999999988753049899999999989999984056883310
Q gi|254780182|r  461 RLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI  520 (910)
Q Consensus       461 rL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I  520 (910)
                      +|.+=|+|+--.++-=++.-+++-+.|++=-+-  ..|.   +.++.+|.. |.+|--+-
T Consensus       199 QLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR--~RWg---qyfrsmK~s-gs~r~ekd  252 (383)
T KOG4577         199 QLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR--TRWG---QYFRSMKRS-GSSRAEKD  252 (383)
T ss_pred             HHHHCCCCCEEEHHHHHHHHHHHHHHHHHHCCH--HHHH---HHHHHHHCC-CCCCCCCC
T ss_conf             850113866133146654116777765430033--5789---998874126-88632123


No 319
>pfam06609 TRI12 Fungal trichothecene efflux pump (TRI12). This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster.It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes.
Probab=21.60  E-value=31  Score=12.23  Aligned_cols=32  Identities=19%  Similarity=0.288  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH
Q ss_conf             67877799886313754000897367899999
Q gi|254780182|r   28 SYLTYAINVILGRAIPDLRDGLKPVHRRILFG   59 (910)
Q Consensus        28 syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~   59 (910)
                      .|+.|-=.+|++-|||.+-+-|....+---|+
T Consensus        53 ~~~~~ld~tivatAlP~I~~dl~~~~~~~W~~   84 (598)
T pfam06609        53 VCATYFVLQASASALPNILQDIGQSENQGLFS   84 (598)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHH
T ss_conf             99999500276634716998708987735499


No 320
>cd04588 CBS_pair_CAP-ED_DUF294_assoc_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the archaeal CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain.  Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site.
Probab=21.60  E-value=36  Score=11.60  Aligned_cols=68  Identities=24%  Similarity=0.266  Sum_probs=36.2

Q ss_pred             HCCCCCCCCCCHH----HHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCC--CCCCCHHHHHHHHHHHCCCHHCCCCCCCC
Q ss_conf             1375400089736----78999999987899999811340425566436--68870478999999712201115613147
Q gi|254780182|r   40 RAIPDLRDGLKPV----HRRILFGMMQMGVEWNKKYVKCARISGEVMGK--YHPHGNAAIYDALARMAQDWSLRLLLIEG  113 (910)
Q Consensus        40 RAlPd~rDGlKpv----~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gk--yHPHGd~siy~a~v~maq~~~~r~plidg  113 (910)
                      +++|=+.|| |++    .|.|+.+..+...  +       .-|+++|.+  +.=|-|.++++|+-.|.+.---+.|.+|.
T Consensus        25 ~~~pVvd~~-~lvGiit~~Di~~~~~~~~~--~-------~~V~~~M~~~~~tv~~d~~l~~~~~~m~~~~v~~l~Vvd~   94 (110)
T cd04588          25 HGAPVVDDG-KLVGIVTLSDIAHAIARGLE--L-------AKVKDVMTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTDD   94 (110)
T ss_pred             CEEEEEECC-EEEEEEEHHHHHHHHHCCCC--C-------CHHHHHCCCCCCEECCCCCHHHHHHHHHHCCCCEEEEEEC
T ss_conf             889999899-99999966898999873797--7-------8034520489729858996999999998779978999966


Q ss_pred             CCCC
Q ss_conf             8870
Q gi|254780182|r  114 QGNF  117 (910)
Q Consensus       114 ~Gnf  117 (910)
                      +|..
T Consensus        95 ~~~l   98 (110)
T cd04588          95 EGRP   98 (110)
T ss_pred             CCEE
T ss_conf             9999


No 321
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=21.59  E-value=37  Score=11.53  Aligned_cols=52  Identities=13%  Similarity=0.150  Sum_probs=34.4

Q ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCCCCCCC
Q ss_conf             9887530498999999999899999840568833100-134345301014567
Q gi|254780182|r  485 KECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIV-EGLLDMEDEDCIVRE  536 (910)
Q Consensus       485 ~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~-~~~~~i~~EdlI~~E  536 (910)
                      .-|+.||+++.+++.++..-+.++..--|..||..=. ..-+.++.--+.|++
T Consensus        66 ~lL~~IL~ne~~ir~Llq~RmdeL~~Li~qs~rQ~~ln~aYg~~sg~~l~p~~  118 (121)
T PRK10548         66 PMLRQILDNESELKQLLQQRMDELSKLIGQSTRQKSVNSAYGQLSGFLLLPDD  118 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCC
T ss_conf             99999998789999999999999999999889999999999705887208998


No 322
>pfam05615 THOC7 Tho complex subunit 7. The Tho complex is involved in transcription elongation and mRNA export from the nucleus.
Probab=21.53  E-value=37  Score=11.52  Aligned_cols=70  Identities=17%  Similarity=0.172  Sum_probs=48.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH---HCCCCC
Q ss_conf             5236999999999878999988879--9999989999999998875304989999999998999998---405688
Q gi|254780182|r  446 TMYLSEVQTRAILELRLARLTGLGR--DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKD---ELDTPR  516 (910)
Q Consensus       446 ~f~lSe~QA~AILdMrL~rLt~LE~--~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~---kygd~R  516 (910)
                      .|.|+-.-++++++|-.+..-+-+.  ..|+.....+.++|++|+.=|..-+..++.-+ |..++.+   .++.+|
T Consensus        53 ~~e~s~~k~q~v~~~n~~E~e~Y~~~~~~I~~~i~~~k~~i~~lk~~L~~Ak~~r~~r~-eyD~La~~I~~~P~~R  127 (135)
T pfam05615        53 ALELSMLKLQFVIEMNERERENYEQEKEEIETTIENAKEEIEELKKELEEAKRERKNRK-EYDELAKKITSQPVTR  127 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCCCCC
T ss_conf             88999999999999999999999999999999999999999999999999999999799-9999999998389981


No 323
>TIGR02404 trehalos_R_Bsub trehalose operon repressor; InterPro: IPR012770    This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from Escherichia coli..
Probab=21.52  E-value=30  Score=12.29  Aligned_cols=147  Identities=13%  Similarity=0.162  Sum_probs=85.0

Q ss_pred             HHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEE----EEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             888863458668874434475889999870120389----9998865433678459999246443528999999999987
Q gi|254780182|r  214 DALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIV----IRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVR  289 (910)
Q Consensus       214 ~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~----iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~  289 (910)
                      .||.+-|.+-++|-|-.+=.-..+.+.|..-||.|+    +-...-.-...+||=.||+.-=+|+.+-+.|+- =.||.+
T Consensus         7 ~dL~~~I~~~~yk~G~~LPSE~~L~~~Y~~SReTvRKAL~~L~~~GyIQKi~GKGsiVl~~~~~~fP~SGivS-y~EL~~   85 (236)
T TIGR02404         7 KDLEQKIDAGQYKEGDLLPSEHELMEQYGASRETVRKALNLLTEAGYIQKIRGKGSIVLNREKYEFPISGIVS-YKELAE   85 (236)
T ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEEEECCCCCCCCCCCCHH-HHHHHH
T ss_conf             9999860057478877388878999860687458899999998578716761523487667631048630011-278776


Q ss_pred             CCCCCHHHHHHHHCCCCCEEEEEEECCCCCHH-HHHHHHHHHCCHHCCCCCEEEEE-----ECCCCCCCCHHHHHHHHHH
Q ss_conf             16650144587303746557999947988778-99999997610110000002455-----4166300029999999999
Q gi|254780182|r  290 EKRIVDIADLRDESDRQGYRVVIELKRGASAD-VILNQLYRYTSLQSLFSVNMVAL-----NGYKPERFTLIGILKAFVA  363 (910)
Q Consensus       290 ~~ki~gI~dirDeSdr~giRivielKr~~~~~-~vln~Lyk~T~Lq~sf~~N~~aL-----~~g~P~~l~Lk~iL~~fi~  363 (910)
                      .-.+            +-.=.|+++-++.-.+ .|=..+...|.|+.   .+..+|     +||++.+|..-=+++.++-
T Consensus        86 ~l~~------------~~~T~V~~~~~e~~~~~~~a~~~~~~tel~~---~~i~~i~R~R~IdGe~~ILD~DYl~~~~vP  150 (236)
T TIGR02404        86 TLGL------------EAKTEVVELQKELPLEESLAKLTGLETELEG---SLIWRIKRVRVIDGEAVILDIDYLLKKLVP  150 (236)
T ss_pred             HCCC------------CEEEEEEECCCCCCCHHHHHHHCCCCCCCCC---CCCEEEEEEEEECCEEEEECCHHHHHHCCC
T ss_conf             4298------------2357787327898870678977056565278---862178998776787566301112101178


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999999
Q gi|254780182|r  364 FREEVVVRRTKYL  376 (910)
Q Consensus       364 hR~evi~rRt~~~  376 (910)
                      +=-.-|-=.+-|+
T Consensus       151 ~l~keiAE~SIY~  163 (236)
T TIGR02404       151 GLTKEIAEDSIYD  163 (236)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             6337898877998


No 324
>KOG0998 consensus
Probab=21.44  E-value=37  Score=11.50  Aligned_cols=52  Identities=17%  Similarity=0.204  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCE
Q ss_conf             8799999989999999998875304989999999998999998405688331
Q gi|254780182|r  468 LGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTR  519 (910)
Q Consensus       468 LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~  519 (910)
                      -|+..+..++.++.++-..|...+.+.....+-+.++|..+..+.++.|.+.
T Consensus       505 ~ei~~~~~~ln~~~qq~~~l~~~v~~~~~~ve~l~~~L~~~~~~~~~~~s~~  556 (847)
T KOG0998         505 REISSLEKELNELQQQLSVLEGSVKAIESQVENLQKELLDLIYEMADTRSKS  556 (847)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
T ss_conf             6688777776656667767764320234424566777999999987640410


No 325
>PRK11779 sbcB exonuclease I; Provisional
Probab=21.39  E-value=37  Score=11.50  Aligned_cols=48  Identities=21%  Similarity=0.223  Sum_probs=25.5

Q ss_pred             EEEEEEECCCC------CHHHHHHHHHHHC-CHH---CCCCCEEEEEECCCCCCCCHHH
Q ss_conf             57999947988------7789999999761-011---0000002455416630002999
Q gi|254780182|r  308 YRVVIELKRGA------SADVILNQLYRYT-SLQ---SLFSVNMVALNGYKPERFTLIG  356 (910)
Q Consensus       308 iRivielKr~~------~~~~vln~Lyk~T-~Lq---~sf~~N~~aL~~g~P~~l~Lk~  356 (910)
                      -.||+.|+.|-      +.+.+...||+.. .|.   ...++-.+.+ +..|.++..+-
T Consensus       256 ~~i~fDL~~DP~~ll~ls~~eL~~~l~t~~~~l~~~~~~~plk~I~i-NK~Pil~p~~~  313 (477)
T PRK11779        256 AVIVCDLAGDPSPLLELDADTLRERLYTRRADLAEGELPVPLKLVHL-NKCPVLAPAKT  313 (477)
T ss_pred             CEEEEECCCCHHHHHCCCHHHHHHHHCCCHHHHHCCCCCCCEEEEEE-CCCCEECCHHH
T ss_conf             65888735797998669999999997154322103467765067530-78880176575


No 326
>pfam02827 PKI cAMP-dependent protein kinase inhibitor. Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of its regulatory chains.
Probab=21.37  E-value=33  Score=12.02  Aligned_cols=23  Identities=26%  Similarity=0.541  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHH--CCCCCCCC
Q ss_conf             876787779988631--37540008
Q gi|254780182|r   26 QNSYLTYAINVILGR--AIPDLRDG   48 (910)
Q Consensus        26 ~~syl~Ya~svI~~R--AlPd~rDG   48 (910)
                      +.+|.+|+.+==.+|  ||||+--.
T Consensus         4 E~~~sdFis~~RtGRRNAvpDI~gs   28 (74)
T pfam02827         4 ESVYSDFISSGRTGRRNALPDIQGS   28 (74)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             1568888870543443445200257


No 327
>KOG2303 consensus
Probab=21.33  E-value=37  Score=11.49  Aligned_cols=40  Identities=15%  Similarity=0.267  Sum_probs=16.2

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEEC-CCCCHHHHHHHHH
Q ss_conf             99999998716650144587303746557999947-9887789999999
Q gi|254780182|r  281 LEKIAELVREKRIVDIADLRDESDRQGYRVVIELK-RGASADVILNQLY  328 (910)
Q Consensus       281 ie~Ia~lv~~~ki~gI~dirDeSdr~giRivielK-r~~~~~~vln~Ly  328 (910)
                      .+++.+.++.+.-.-+.|+|-        |+-..+ -..||..+.|++|
T Consensus       373 C~~V~~av~~g~eqv~~Dvr~--------i~~~~~~~p~dp~~l~nri~  413 (706)
T KOG2303         373 CRQVCKAVQSGDEQVLADVRR--------IVNDISYTPTDPADLCNRIL  413 (706)
T ss_pred             HHHHHHHHHCCCHHHHHHHHH--------HHCCCCCCCCCHHHHHHHHH
T ss_conf             999999997473654320687--------71488868889899987666


No 328
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain  HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.27  E-value=37  Score=11.48  Aligned_cols=40  Identities=13%  Similarity=0.236  Sum_probs=21.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             23699999999987899998887999999899999999988753
Q gi|254780182|r  447 MYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDI  490 (910)
Q Consensus       447 f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~I  490 (910)
                      ++||-.+...+|+.....+.    .-+++..+++.++|++|+.|
T Consensus        56 ~G~~L~eIk~~l~~~~~~~~----~~l~~~~~~i~~~I~~L~~l   95 (96)
T cd04768          56 LGFSLAEIKELLDTEMEELT----AMLLEKKQAIQQKIDRLQQL   95 (96)
T ss_pred             CCCCHHHHHHHHCCCCHHHH----HHHHHHHHHHHHHHHHHHHC
T ss_conf             79999999999939969999----99999999999999999821


No 329
>PRK10580 proY putative proline-specific permease; Provisional
Probab=21.27  E-value=37  Score=11.48  Aligned_cols=39  Identities=13%  Similarity=0.146  Sum_probs=17.5

Q ss_pred             HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             016761010133178985478999999887618776888
Q gi|254780182|r  176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLD  214 (910)
Q Consensus       176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~  214 (910)
                      -+|-.|+..+++.-+-.+-=-|.+--+-.=.+||.-++.
T Consensus       195 ~~g~~g~~~a~~~~~faf~G~e~i~~~a~E~knP~r~iP  233 (457)
T PRK10580        195 SNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIP  233 (457)
T ss_pred             CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHH
T ss_conf             644789999999999998289999999886208666799


No 330
>pfam09220 LA-virus_coat L-A virus, major coat protein. Members of this family form the major coat protein of the Saccharomyces cerevisiae L-A virus.
Probab=21.14  E-value=28  Score=12.63  Aligned_cols=67  Identities=13%  Similarity=0.109  Sum_probs=26.8

Q ss_pred             HHHHHHCCCCCEEEEEEE----CCC------C-CHHHHHHHHHHHCCHHCCCCCEE----EEEECCCCCCCCHHHHHHHH
Q ss_conf             458730374655799994----798------8-77899999997610110000002----45541663000299999999
Q gi|254780182|r  297 ADLRDESDRQGYRVVIEL----KRG------A-SADVILNQLYRYTSLQSLFSVNM----VALNGYKPERFTLIGILKAF  361 (910)
Q Consensus       297 ~dirDeSdr~giRiviel----Kr~------~-~~~~vln~Lyk~T~Lq~sf~~N~----~aL~~g~P~~l~Lk~iL~~f  361 (910)
                      -|+|-.+-.+ .+||+-.    |+.      . .|+.--.-.|++..--.++.-=.    ++=.-+-|.--=....|+-|
T Consensus       201 iDlR~Lt~~E-a~~VLmM~~eWk~qTn~klDf~~p~La~ki~YR~~~~i~~~~~Wl~~~~~~~~~~~P~s~v~~SALrKY  279 (436)
T pfam09220       201 LDVRPLTVTE-VNFVLMMMSKWHRRTNLAIDYEAPQLADKFAYRHALTVQDADEWIEGDRTDDQFRPPSSKVMLSALRKY  279 (436)
T ss_pred             EECCCCCHHH-HEEEEEECCCCCCCCCEEECCCCHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             3347798546-215565214545554324413677788999887418813455442565557667899417899999999


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780182|r  362 VAF  364 (910)
Q Consensus       362 i~h  364 (910)
                      +.|
T Consensus       280 V~~  282 (436)
T pfam09220       280 VNH  282 (436)
T ss_pred             HHC
T ss_conf             841


No 331
>PRK12808 flagellin; Provisional
Probab=21.11  E-value=38  Score=11.45  Aligned_cols=62  Identities=24%  Similarity=0.306  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             89999998740699999986189978987877631269788999997402211122234452369999999998789999
Q gi|254780182|r  386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL  465 (910)
Q Consensus       386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL  465 (910)
                      -+.||-.|..|...-|.++.-      |-..|-+                                  ...||. |+|.|
T Consensus        55 qi~gl~qa~~Na~dgiS~~qt------AEgal~e----------------------------------v~~iLq-RmReL   93 (460)
T PRK12808         55 RESGLGVAANNTQDGMSLIRT------ADSAMNS----------------------------------VSNILL-RMRDL   93 (460)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH------HHHHHHH----------------------------------HHHHHH-HHHHH
T ss_conf             998899999989989999999------9999999----------------------------------999999-99999


Q ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------88879999998999999999887
Q gi|254780182|r  466 ---------TGLGRDDIRNELNSLGIEIKECL  488 (910)
Q Consensus       466 ---------t~LE~~kl~~E~~eL~~~I~~l~  488 (910)
                               +.-++..|+.|+.+|..+|..+-
T Consensus        94 AVQAANgTns~~DR~aiQ~Ei~qL~~EIdrIa  125 (460)
T PRK12808         94 ANQSANGTNTDKNQAALQKEFAELQKQIDYIA  125 (460)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99861566887889999999999999999998


No 332
>KOG0306 consensus
Probab=21.08  E-value=38  Score=11.44  Aligned_cols=93  Identities=12%  Similarity=0.193  Sum_probs=46.0

Q ss_pred             CCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECC------CCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCC-
Q ss_conf             68717999947991898423686204777227866158------98578889618982699993698599975876235-
Q gi|254780182|r  643 WNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDS------RDEILSVETCTQENDILLTTKLGQCVRFPISAIRV-  715 (910)
Q Consensus       643 ~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLke------gD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~-  715 (910)
                      .++.+++.++++-.||-..+.-......+..+.++|+.      .|.+..+..+.++..+++.=-+..+-.|-.+.+.- 
T Consensus       464 pD~~g~vT~saDktVkfWdf~l~~~~~gt~~k~lsl~~~rtLel~ddvL~v~~Spdgk~LaVsLLdnTVkVyflDtlKFf  543 (888)
T KOG0306         464 PDNKGFVTGSADKTVKFWDFKLVVSVPGTQKKVLSLKHTRTLELEDDVLCVSVSPDGKLLAVSLLDNTVKVYFLDTLKFF  543 (888)
T ss_pred             CCCCCEEEECCCCEEEEEEEEEEECCCCCCCEEEEECCCEEEECCCCEEEEEECCCCCEEEEEECCCEEEEEEECCEEEE
T ss_conf             88886087328737999767999426764210454011207843662789997699848988732675799996251446


Q ss_pred             --CCCCCCCCEEEEECCCCCEEE
Q ss_conf             --478665535767528998699
Q gi|254780182|r  716 --FAGRNSVGVRGISLAKGDQVI  736 (910)
Q Consensus       716 --~~GR~a~GVkgIkL~~~D~Vv  736 (910)
                        +-| -+--|..|.+..+.+.+
T Consensus       544 lsLYG-HkLPV~smDIS~DSkli  565 (888)
T KOG0306         544 LSLYG-HKLPVLSMDISPDSKLI  565 (888)
T ss_pred             EEECC-CCCCEEEEECCCCCCEE
T ss_conf             54315-65643688506886737


No 333
>pfam08961 DUF1875 Domain of unknown function (DUF1875). The MIT domain, found in Nuclear receptor-binding factor 2, has no known function.
Probab=21.04  E-value=38  Score=11.44  Aligned_cols=40  Identities=23%  Similarity=0.244  Sum_probs=23.1

Q ss_pred             CCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             699999999987899-9988879999998999999999887
Q gi|254780182|r  449 LSEVQTRAILELRLA-RLTGLGRDDIRNELNSLGIEIKECL  488 (910)
Q Consensus       449 lSe~QA~AILdMrL~-rLt~LE~~kl~~E~~eL~~~I~~l~  488 (910)
                      .-|.||..|.|++-. -.---|-+.|+.|-+.|.++.+.|.
T Consensus       123 ~iEEQaT~IadLkr~Ve~LvaeNerLrkENkqL~AekaRL~  163 (243)
T pfam08961       123 IIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLL  163 (243)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89998877999999999998600999998888868998875


No 334
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=20.99  E-value=38  Score=11.43  Aligned_cols=45  Identities=13%  Similarity=0.023  Sum_probs=18.8

Q ss_pred             CCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2369999999998789-99988879999998999999999887530
Q gi|254780182|r  447 MYLSEVQTRAILELRL-ARLTGLGRDDIRNELNSLGIEIKECLDIL  491 (910)
Q Consensus       447 f~lSe~QA~AILdMrL-~rLt~LE~~kl~~E~~eL~~~I~~l~~IL  491 (910)
                      ++||-.+...+|+.+- +.+..-....|+++.++|.+..+.|+.+|
T Consensus        56 ~G~sL~eIk~lL~~~~~~~~l~~~~~~i~~~I~~L~~~r~~L~~ll  101 (102)
T cd04775          56 GGLPLEEIAGCLAQPHVQAILEERLQSLNREIQRLRQQQQVLAAIL  101 (102)
T ss_pred             CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6999999999985995799999999999999999999999999873


No 335
>PRK09109 motC flagellar motor protein; Reviewed
Probab=20.97  E-value=38  Score=11.43  Aligned_cols=26  Identities=19%  Similarity=0.267  Sum_probs=17.4

Q ss_pred             CHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             28999999999987166501445873
Q gi|254780182|r  276 NKAAMLEKIAELVREKRIVDIADLRD  301 (910)
Q Consensus       276 nk~~lie~Ia~lv~~~ki~gI~dirD  301 (910)
                      +...+++.+.++.+.-+-+|+..+-+
T Consensus        73 ~~~~~i~~l~~la~~aR~~GllaLE~   98 (246)
T PRK09109         73 DLEGGIDRIVEWSMTARKEGLLGLED   98 (246)
T ss_pred             CHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf             99999999999999997645311566


No 336
>COG4168 SapB ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]
Probab=20.95  E-value=38  Score=11.42  Aligned_cols=105  Identities=24%  Similarity=0.376  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCH---HHHHHHHHHHCCCHHCCCCCCCCCCCCC--CCCCCCCC
Q ss_conf             678999999987899999811340425566436688704---7899999971220111561314788708--87769720
Q gi|254780182|r   52 VHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGN---AAIYDALARMAQDWSLRLLLIEGQGNFG--SVDGDPPA  126 (910)
Q Consensus        52 v~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd---~siy~a~v~maq~~~~r~plidg~GnfG--s~dgd~~A  126 (910)
                      +-|||++-.--+=+         -..||-++.-+.||..   +++|++-+--     .. -|  -||+||  |+.|+|-+
T Consensus         5 tlR~ill~~ltLli---------Lslvgfsl~~fdP~apl~~~~l~~g~~~y-----~~-~L--lq~dFGis~~nG~pi~   67 (321)
T COG4168           5 TLRRILLLILTLLI---------LTLVGFSLSYFDPHAPLQGASLWQGWVFY-----FN-GL--LQWDFGISSINGQPIA   67 (321)
T ss_pred             HHHHHHHHHHHHHH---------HHHHHHHHHHCCCCCCHHHHHHHHHHHHH-----HH-HH--HCCCCCCCCCCCCHHH
T ss_conf             99999999999999---------99998885213899730130699999999-----98-88--5203252156980089


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCC----CCHHCCCCCEEEHHHHCCCCCCHHHHHHHH
Q ss_conf             1357899978999999863076840533068988548503432273----211016761010133178985478999999
Q gi|254780182|r  127 AERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYP----NVLVNGGGGIAVGMATNIPTHNLGEVVDGC  202 (910)
Q Consensus       127 A~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P----~lL~nG~~GIAvGmaTnippHNl~Ev~~a~  202 (910)
                      +             .++.                     |+|+..-    .+..-=--||-+||-.-+-.|-.-+..=.+
T Consensus        68 ~-------------~l~~---------------------vfPaT~ELC~~af~lal~~GiPlG~iagv~~~kw~d~~i~~  113 (321)
T COG4168          68 E-------------QLLE---------------------VFPATMELCFLAFGLALIVGIPLGMIAGVTRHKWLDKLISA  113 (321)
T ss_pred             H-------------HHHH---------------------HCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHHHHHH
T ss_conf             9-------------9998---------------------66618999999999999984647988775423078899999


Q ss_pred             HHHHH
Q ss_conf             88761
Q gi|254780182|r  203 VAVID  207 (910)
Q Consensus       203 ~~~i~  207 (910)
                      ++++-
T Consensus       114 is~~G  118 (321)
T COG4168         114 ISLLG  118 (321)
T ss_pred             HHHHC
T ss_conf             99854


No 337
>cd04642 CBS_pair_29 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=20.91  E-value=38  Score=11.42  Aligned_cols=25  Identities=20%  Similarity=0.328  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHCCCHHCCCCCCCCCC
Q ss_conf             7899999971220111561314788
Q gi|254780182|r   91 AAIYDALARMAQDWSLRLLLIEGQG  115 (910)
Q Consensus        91 ~siy~a~v~maq~~~~r~plidg~G  115 (910)
                      +++.+|+-.|++.---..|.+|.+|
T Consensus        10 ~~l~eA~~lm~~~~i~~lPVvd~~g   34 (126)
T cd04642          10 ERVLDAFKLMRKNNISGLPVVDEKG   34 (126)
T ss_pred             CCHHHHHHHHHHCCCCEEEEEECCC
T ss_conf             9999999999980987899992899


No 338
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.79  E-value=38  Score=11.40  Aligned_cols=14  Identities=14%  Similarity=0.420  Sum_probs=6.6

Q ss_pred             HHHCCCCCHHHHHH
Q ss_conf             76187768888886
Q gi|254780182|r  205 VIDNPDIDLDALME  218 (910)
Q Consensus       205 ~i~~p~~~~~eL~~  218 (910)
                      +++..+++.++|-+
T Consensus        27 l~~kge~tDeela~   40 (176)
T COG1675          27 LLEKGELTDEELAE   40 (176)
T ss_pred             HHHCCCCCHHHHHH
T ss_conf             87527767489988


No 339
>COG0082 AroC Chorismate synthase [Amino acid transport and metabolism]
Probab=20.77  E-value=31  Score=12.19  Aligned_cols=64  Identities=20%  Similarity=0.250  Sum_probs=38.3

Q ss_pred             HHHHHHCCHHCCCCCEEEEEECCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999761011000000245541663000299-99999999999999999999999998887789999
Q gi|254780182|r  325 NQLYRYTSLQSLFSVNMVALNGYKPERFTLI-GILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGL  390 (910)
Q Consensus       325 n~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk-~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL  390 (910)
                      -+||+.|-.=.|-+.-+-|++||.|--|.|. +.++.+++-|+--.-|-+  .-++-.++.+||-|.
T Consensus         6 G~~fr~tT~GESHG~alg~VIdG~PaGl~l~~edIq~eL~RRrpG~~r~~--t~R~E~D~veIlSGv   70 (369)
T COG0082           6 GRLFRVTTFGESHGPALGAVIDGCPAGLELSEEDIQKELDRRRPGYSRGT--TMRKEKDEVEILSGV   70 (369)
T ss_pred             CCEEEEEEECCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCC--CCCCCCCCEEEEEEE
T ss_conf             54179875005678735899935599970699999999974479988875--545678614880015


No 340
>TIGR01296 asd_B aspartate-semialdehyde dehydrogenase; InterPro: IPR005986   Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see .   Aspartate-semialdehyde dehydrogenase, the second enzyme in the aspartate pathway, converts aspartyl phosphate to aspartate-semialdehyde, the branch point intermediate between the lysine and threonine/methionine pathways. Based on sequence alignments, the aspartate-semialdehyde dehydrogenase family appears to have two distinct subgroups, one found in most bacteria (Gram-positve and Gram-negative), while the other is found primarily in organisms lacking peptidoglycan (archaea,fungi and some bacteria). Most studies have been performed on enzymes isolated from Gram-negative bacteria , , , . The N-terminal domain forms the active site and NADP-binding pocket, while C-terminal domain is primarily involved in hydrophobic intersubunit contacts. The catalytic mechanism involves the formation of a covalent thioester acyl-enzyme intermediate mediated through nucleophilic attack by an active site cysteine residue on the substrate aspartyl phosphate. Release of inorganic phosphate is followed by hydride transfer from NADPH to yield the product. The recently described archaeal structure suggests that the two subgroups of aspartate semi-aldehyde dehydrogenase share similar structures and have an identical catalytic mechanism, despite their relatively low sequence identity . Unlike the bacterial enzymes, the archaeal enzyme utilised both NAD and NADP as cofactor.   This entry represents the subgroup of aspartate-semialdehyde dehydrogenase most commonly found in bacteria. Note that some bacteria, such as Chlamydia, contain the enzyme from the other subgroup (IPR005676 from INTERPRO) instead.; GO: 0004073 aspartate-semialdehyde dehydrogenase activity, 0009086 methionine biosynthetic process, 0009088 threonine biosynthetic process.
Probab=20.71  E-value=30  Score=12.39  Aligned_cols=58  Identities=22%  Similarity=0.335  Sum_probs=29.8

Q ss_pred             CEEEEEEC------CCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCC-----------CEEEEEEEECCC
Q ss_conf             68999972------89964999945998999990105544515687388980899-----------879999983566
Q gi|254780182|r  840 ALVAVFPV------NDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKD-----------ERVVSVERIRES  900 (910)
Q Consensus       840 ~lv~~~~V------~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~-----------D~Vv~va~i~~~  900 (910)
                      -.|++++|      ....-|-+-+++..   +.+.++++.=++|.||.+++-..+           .-=++|.||..+
T Consensus       240 ~~vSaTCVRvPVf~GHS~S~~iEf~~d~---~~~e~~~E~Lk~ApGV~~~D~P~~~~Yp~P~~A~G~D~VfVGRIRkD  314 (350)
T TIGR01296       240 LKVSATCVRVPVFTGHSESVNIEFEKDE---ISPEDVREVLKNAPGVVVIDDPSQNLYPTPLEAVGEDEVFVGRIRKD  314 (350)
T ss_pred             CCEEEEEEECCCHHCCHHHHHHHHCCCC---CCHHHHHHHHCCCCEEEEEECCCCCCCCCCHHEECCCCEEEEEEECC
T ss_conf             4451578874111111232100111688---78889999734798679987688877888310102571567544447


No 341
>pfam09417 consensus
Probab=20.70  E-value=38  Score=11.38  Aligned_cols=13  Identities=46%  Similarity=0.552  Sum_probs=11.3

Q ss_pred             CCCHHHHHHHHHH
Q ss_conf             3699999999987
Q gi|254780182|r  448 YLSEVQTRAILEL  460 (910)
Q Consensus       448 ~lSe~QA~AILdM  460 (910)
                      .|||.|.++||++
T Consensus       108 R~tEe~~e~il~~  120 (121)
T pfam09417       108 RFTEEQIEEILEL  120 (121)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             5998999999975


No 342
>KOG0207 consensus
Probab=20.65  E-value=38  Score=11.38  Aligned_cols=26  Identities=12%  Similarity=0.123  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99888778999999874069999998
Q gi|254780182|r  379 KARDRAHVLVGLAIAVANLDEVVRII  404 (910)
Q Consensus       379 ka~~R~HILeGL~~Al~nIDeVI~iI  404 (910)
                      +-..+.-+..|+.+++--+--+...+
T Consensus       233 ~w~~~fl~s~~~~~~v~~~~~~~~~~  258 (951)
T KOG0207         233 KWKRPFLISLGFSLPVSFAMIICPPL  258 (951)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             61168899999999999999986543


No 343
>TIGR00058 Hemerythrin hemerythrin family non-heme iron proteins; InterPro: IPR002063   The hemerythrin family is composed of hemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Hemerythrin is an oxygen-binding protein found in the vascular system and coelemic fluid, or in muscles (myohemerythrin) in invertebrates . Many of the lhomologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (IPR000160 from INTERPRO) and methyl-accepting chemotaxis protein (MCP) signalling domain (IPR004089 from INTERPRO). Most hemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.   Hemerythrins and myohemerythrins ,  are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-alpha-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces . In both hemerythrins and myohemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains , 5 His, 1 Glu and 1 Asp . Ovohemerythrin , a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal .   This entry represents the hemerythrin family of proteins.; GO: 0005344 oxygen transporter activity, 0005506 iron ion binding, 0006810 transport.
Probab=20.63  E-value=37  Score=11.57  Aligned_cols=42  Identities=17%  Similarity=0.230  Sum_probs=20.6

Q ss_pred             CCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0299999999999--9999999999999999888778999999874
Q gi|254780182|r  352 FTLIGILKAFVAF--REEVVVRRTKYLLNKARDRAHVLVGLAIAVA  395 (910)
Q Consensus       352 l~Lk~iL~~fi~h--R~evi~rRt~~~L~ka~~R~HILeGL~~Al~  395 (910)
                      -+|++++++...|  -.|..=.+++|.=-..=+..|  +||+-++.
T Consensus        40 ~~Lk~l~~v~~~HF~~EE~~M~~a~Y~~~~~HK~~H--~~F~~~~~   83 (116)
T TIGR00058        40 TALKELIDVTVKHFLDEEAMMEAANYSDYDEHKKAH--DDFLAKLR   83 (116)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH--HHHHHHHC
T ss_conf             678899999998668899999887227875358999--99999723


No 344
>PRK06321 replicative DNA helicase; Provisional
Probab=20.56  E-value=39  Score=11.36  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             8999999999899999840568
Q gi|254780182|r  494 RSRLLGIIKQELLSVKDELDTP  515 (910)
Q Consensus       494 ~~~l~~iI~~EL~eik~kygd~  515 (910)
                      +......|-..|+.+.+.++-|
T Consensus       360 r~~~i~~isr~lK~lAkel~vp  381 (472)
T PRK06321        360 RQTEISEISRMLKNLARELNIP  381 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999999999999999997997


No 345
>TIGR02976 phageshock_pspB phage shock protein B; InterPro: IPR009554   This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages . Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one ..
Probab=20.53  E-value=39  Score=11.36  Aligned_cols=25  Identities=16%  Similarity=0.226  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             9999989999999998875304989
Q gi|254780182|r  471 DDIRNELNSLGIEIKECLDILSSRS  495 (910)
Q Consensus       471 ~kl~~E~~eL~~~I~~l~~IL~s~~  495 (910)
                      ..|.+..+.|.++|+.||.||.++.
T Consensus        45 ~~L~~~A~Rl~~Ri~tLE~iLd~e~   69 (75)
T TIGR02976        45 QELYAKADRLEERIDTLERILDAEH   69 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999999899999999999872048


No 346
>pfam09942 DUF2174 Uncharacterized conserved protein (DUF2174). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=20.52  E-value=31  Score=12.24  Aligned_cols=13  Identities=23%  Similarity=0.818  Sum_probs=10.5

Q ss_pred             HCCCCCCCCCCCC
Q ss_conf             1156131478870
Q gi|254780182|r  105 SLRLLLIEGQGNF  117 (910)
Q Consensus       105 ~~r~plidg~Gnf  117 (910)
                      .|+|..||||||=
T Consensus        25 ~~~fl~idG~GdP   37 (83)
T pfam09942        25 AMNFLMVDGKGDP   37 (83)
T ss_pred             CCCEEEEEEECCC
T ss_conf             9537987403599


No 347
>pfam02502 LacAB_rpiB Ribose/Galactose Isomerase. This family of proteins contains the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB).
Probab=20.52  E-value=35  Score=11.76  Aligned_cols=40  Identities=23%  Similarity=0.145  Sum_probs=19.7

Q ss_pred             CCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             000245541663000299999999999999999999999999
Q gi|254780182|r  338 SVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNK  379 (910)
Q Consensus       338 ~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~k  379 (910)
                      ++|.+||=...-..--.++|++.|++..++  --|-+-+++|
T Consensus        99 naNVl~lG~r~~~~~~a~~iv~~fl~t~F~--ggRh~~Rv~k  138 (140)
T pfam02502        99 NANVLCLGARVIGPELAKEIVDAFLATEFE--GGRHARRVDK  138 (140)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHCCCCC--CCCHHHHHHH
T ss_conf             985899765324999999999999769988--8637999986


No 348
>PRK05469 peptidase T; Provisional
Probab=20.51  E-value=39  Score=11.35  Aligned_cols=59  Identities=22%  Similarity=0.353  Sum_probs=22.7

Q ss_pred             CEECCCCC-----CCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCC----CHHHHHHHHHHHHHCCCC
Q ss_conf             33068988-----548503432273211016761010133178985----478999999887618776
Q gi|254780182|r  153 FRPNYDGS-----FQEPVVLCARYPNVLVNGGGGIAVGMATNIPTH----NLGEVVDGCVAVIDNPDI  211 (910)
Q Consensus       153 ~~~n~D~~-----~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippH----Nl~Ev~~a~~~~i~~p~~  211 (910)
                      .+.||||.     ..+-+.=|+.||.|.---...|=+.=-|.+---    -+-++++++..+.++|++
T Consensus        94 v~~nYdG~di~l~~~~~~l~~~~~P~L~~~~G~~iI~sdGtTlLGADDKAGIA~Ime~~~~L~e~~~i  161 (405)
T PRK05469         94 IIENYDGGDIALGIGNEVLSPAEFPELKNYIGQTLITTDGTTLLGADDKAGIAEIMTALEYLIAHPEI  161 (405)
T ss_pred             EEECCCCCCEEECCCCCEECHHHCCHHHHHCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             97367887234068870765564813676159857967997112343388999999999999868999


No 349
>TIGR01992 PTS-IIBC-Tre PTS system, trehalose-specific IIBC component; InterPro: IPR011296   This entry represents the fused enzyme II B and C components of the trehalose-specific PTS sugar transporter system . Trehalose is converted to trehalose-6-phosphate in the process of translocation into the cell. These transporters lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr) . The exceptions to this rule are Staphylococci and Streptococci which contain their own A domain as a C-terminal fusion. This family is closely related to the sucrose transporting PTS IIBC enzymes described by the IIB component and the IIC component (IPR004719 from INTERPRO), respectively. In Escherichia coli, Bacillus subtilis and Pseudomonas fluorescens the presence of this gene is associated with the presence of trehalase which degrades T6P to glucose and glucose-6-P. Trehalose may also be transported (in Salmonella) via the mannose PTS or galactose permease systems , or (in Sinorhizobium, Thermococcus and Sulfolobus, for instance) by ABC transporters , , .; GO: 0015574 trehalose transmembrane transporter activity, 0015771 trehalose transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=20.32  E-value=39  Score=11.32  Aligned_cols=51  Identities=24%  Similarity=0.517  Sum_probs=37.2

Q ss_pred             CCHHHHHHHH----HHHHHCCCCCHHHHHH--HCCCCCCCCCC---CCCCHHHHHHHHHHC
Q ss_conf             5478999999----8876187768888886--34586688744---344758899998701
Q gi|254780182|r  193 HNLGEVVDGC----VAVIDNPDIDLDALME--IIRGPDFPTGA---VILGRTGIKNAYATG  244 (910)
Q Consensus       193 HNl~Ev~~a~----~~~i~~p~~~~~eL~~--~i~GPDFPTGG---~I~~~~~i~~~y~tG  244 (910)
                      -|+..+..|+    .+|.|+.++..++|=+  .+|| -|-|+|   +|+|.....+.|+.=
T Consensus        15 eNi~~atHCvTRLRfvL~D~~~v~~~~l~~~~~VKG-~F~~~GQFQVvIGpg~V~~~Y~~l   74 (489)
T TIGR01992        15 ENIEAATHCVTRLRFVLKDPSKVDVEALEQIDLVKG-SFTTAGQFQVVIGPGDVEKVYAEL   74 (489)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCC-EEECCCEEEEEECCCCHHHHHHHH
T ss_conf             016687568888888616813378567636882244-142485279986379879999999


No 350
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=20.31  E-value=39  Score=11.32  Aligned_cols=46  Identities=4%  Similarity=-0.021  Sum_probs=30.9

Q ss_pred             HHHHCCCCCCCCCCH-HHHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHC
Q ss_conf             863137540008973-678999999987899999811----34042556643
Q gi|254780182|r   37 ILGRAIPDLRDGLKP-VHRRILFGMMQMGVEWNKKYV----KCARISGEVMG   83 (910)
Q Consensus        37 I~~RAlPd~rDGlKp-v~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~g   83 (910)
                      -|||+|=+- .+..| ...||+=++.+||..|+..-+    +..+.+|-++.
T Consensus        17 TVSrvLn~~-~~Vs~~Tr~rV~~aa~eLgY~pn~~Ar~L~~~~s~~Igviv~   67 (335)
T PRK10703         17 TVSHVINKT-RFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLAT   67 (335)
T ss_pred             HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCEEEEEEC
T ss_conf             999996896-998999999999999982999787787541177745999954


No 351
>COG5184 ATS1 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]
Probab=20.29  E-value=39  Score=11.32  Aligned_cols=18  Identities=11%  Similarity=0.224  Sum_probs=8.0

Q ss_pred             ECCCCCEEEEEECCCEEE
Q ss_conf             618982699993698599
Q gi|254780182|r  689 TCTQENDILLTTKLGQCV  706 (910)
Q Consensus       689 ~~~~~~~Iil~T~~G~~l  706 (910)
                      ++.+.++++++|+.|++-
T Consensus       236 la~G~dh~i~lt~~G~vy  253 (476)
T COG5184         236 LAAGADHLIALTNEGKVY  253 (476)
T ss_pred             ECCCCCEEEEEECCCCEE
T ss_conf             205885399993598288


No 352
>PRK00574 gltX glutamyl-tRNA synthetase; Reviewed
Probab=20.27  E-value=39  Score=11.31  Aligned_cols=17  Identities=18%  Similarity=0.602  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHCCCCCCC
Q ss_conf             78999999987899999
Q gi|254780182|r   53 HRRILFGMMQMGVEWNK   69 (910)
Q Consensus        53 ~Rrily~m~~~~~~~~~   69 (910)
                      -..|+=+|..+|+.+|-
T Consensus        56 ~~~I~~~L~wlgl~~DE   72 (489)
T PRK00574         56 EESQLENLKWLGIDWDE   72 (489)
T ss_pred             HHHHHHHHHHCCCCCCC
T ss_conf             99999999987988877


No 353
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=20.26  E-value=25  Score=13.05  Aligned_cols=35  Identities=31%  Similarity=0.547  Sum_probs=28.1

Q ss_pred             CCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             32110167610101331789854789999998876187
Q gi|254780182|r  172 PNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNP  209 (910)
Q Consensus       172 P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p  209 (910)
                      |.+-.=|+-|+|+|+|-.   -.|+.++.++.-++++|
T Consensus        95 sl~A~~G~~GlaIGlAlQ---~~lsN~~sGi~Il~~rp  129 (285)
T PRK10334         95 SVIAVLGAAGLAVGLALQ---GSLSNLAAGVLLVMFRP  129 (285)
T ss_pred             HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHCCCC
T ss_conf             999999999999999999---99999998758640388


No 354
>KOG2230 consensus
Probab=20.22  E-value=39  Score=11.31  Aligned_cols=39  Identities=21%  Similarity=0.375  Sum_probs=18.9

Q ss_pred             CCCCCCHHHHHHHHH--HHHHCCCCCHHHHHHHCCCCCCCCCCCC
Q ss_conf             789854789999998--8761877688888863458668874434
Q gi|254780182|r  189 NIPTHNLGEVVDGCV--AVIDNPDIDLDALMEIIRGPDFPTGAVI  231 (910)
Q Consensus       189 nippHNl~Ev~~a~~--~~i~~p~~~~~eL~~~i~GPDFPTGG~I  231 (910)
                      +.||--..++-.+-|  .+|+...++-    ..==||-|||-||=
T Consensus       161 svPPdC~p~iyhGECH~NfiRK~Q~SF----sWDWGPsfPt~GI~  201 (867)
T KOG2230         161 SLPPDCNPDIYHGECHQNFIRKAQYSF----AWDWGPSFPTVGIP  201 (867)
T ss_pred             CCCCCCCCHHHCCCHHHHHHHHHHCCE----ECCCCCCCCCCCCC
T ss_conf             799898950011604788998754004----11347788667887


No 355
>PRK06223 malate dehydrogenase; Reviewed
Probab=20.19  E-value=39  Score=11.30  Aligned_cols=35  Identities=14%  Similarity=0.240  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999878999988879999998999999999887530
Q gi|254780182|r  454 TRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDIL  491 (910)
Q Consensus       454 A~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL  491 (910)
                      .+.|+++   .|+..|++++++=.+.|++.++.++++|
T Consensus       277 i~~i~~l---~L~~~E~~~l~~sa~~i~~~~~~vk~ll  311 (312)
T PRK06223        277 VEKVIEI---ELTEDEKEAFDKSVEAVKKLCEALKSIL  311 (312)
T ss_pred             EEEECCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             5998389---9999999999999999999999998458


No 356
>KOG1891 consensus
Probab=20.12  E-value=38  Score=11.39  Aligned_cols=25  Identities=32%  Similarity=0.555  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf             9999999899999840568833100
Q gi|254780182|r  497 LLGIIKQELLSVKDELDTPRRTRIV  521 (910)
Q Consensus       497 l~~iI~~EL~eik~kygd~RRT~I~  521 (910)
                      +.++.++||..|.++|-.=||..|.
T Consensus       233 l~~LfkqEl~~IVk~YErYRrALil  257 (271)
T KOG1891         233 LMKLFKQELFDIVKKYERYRRALIL  257 (271)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999998


No 357
>PRK12584 flagellin A; Reviewed
Probab=20.09  E-value=39  Score=11.29  Aligned_cols=62  Identities=19%  Similarity=0.210  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             89999998740699999986189978987877631269788999997402211122234452369999999998789999
Q gi|254780182|r  386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL  465 (910)
Q Consensus       386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL  465 (910)
                      -+.||-.|..|.-.-|.+++.++      -.|-+                                .  ..||. |+|.|
T Consensus        57 QI~gL~qA~rNa~DgiSliQTAE------GAL~e--------------------------------v--~~iLq-RmREL   95 (510)
T PRK12584         57 QASSLGQAIANTNDGMGIIQVAD------KAMDE--------------------------------Q--LKILD-TVKVK   95 (510)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH------HHHHH--------------------------------H--HHHHH-HHHHH
T ss_conf             99889999884887999999999------99999--------------------------------9--99999-99999


Q ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------88879999998999999999887
Q gi|254780182|r  466 ---------TGLGRDDIRNELNSLGIEIKECL  488 (910)
Q Consensus       466 ---------t~LE~~kl~~E~~eL~~~I~~l~  488 (910)
                               +.-+|.-|++|+++|..+|.++-
T Consensus        96 AVQAAN~tns~~dR~aiQ~Ei~qL~~EIdRIa  127 (510)
T PRK12584         96 ATQAAQDGQTTESRKAIQSDIVRLIQGLDNIG  127 (510)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99860388988899999999999999985662


No 358
>PRK11706 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional
Probab=20.06  E-value=39  Score=11.28  Aligned_cols=21  Identities=14%  Similarity=0.393  Sum_probs=14.1

Q ss_pred             HHHHHHHHHCCCCCHHHHHHH
Q ss_conf             999999987166501445873
Q gi|254780182|r  281 LEKIAELVREKRIVDIADLRD  301 (910)
Q Consensus       281 ie~Ia~lv~~~ki~gI~dirD  301 (910)
                      +++|.++.++..|.-|.|-..
T Consensus       135 ~~~I~~iak~~~i~vIEDaA~  155 (375)
T PRK11706        135 MDTIMALAKKHNLFVVEDAAQ  155 (375)
T ss_pred             HHHHHHHHHHCCCEEEECCCC
T ss_conf             899999885379089834400


No 359
>pfam08820 DUF1803 Domain of unknown function (DUF1803). This small domain is found in one or two copies in proteins from bacteria. The function of this domain is unknown.
Probab=20.02  E-value=39  Score=11.27  Aligned_cols=11  Identities=18%  Similarity=0.395  Sum_probs=4.9

Q ss_pred             HHHHHHHCCCC
Q ss_conf             99999840568
Q gi|254780182|r  505 LLSVKDELDTP  515 (910)
Q Consensus       505 L~eik~kygd~  515 (910)
                      |+++|+.|.+.
T Consensus        31 LR~iKk~f~~q   41 (94)
T pfam08820        31 LRQIKKDFADQ   41 (94)
T ss_pred             HHHHHHHCCCC
T ss_conf             99999876540


No 360
>PRK09848 glucuronide transporter; Provisional
Probab=20.01  E-value=39  Score=11.27  Aligned_cols=31  Identities=13%  Similarity=0.080  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9878999988879999998999999999887
Q gi|254780182|r  458 LELRLARLTGLGRDDIRNELNSLGIEIKECL  488 (910)
Q Consensus       458 LdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~  488 (910)
                      +=|..++||+=...++++|+++-++.-+++.
T Consensus       422 ~~~~~Y~Lt~~~~~eI~~eL~~rr~~~~~~~  452 (457)
T PRK09848        422 VIIWFYPLTDKKFKEIVVEIDNRKKVQQQLI  452 (457)
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9998615889999999999999999876533


Done!