Query         gi|254780124|ref|YP_003064537.1| hypothetical protein CLIBASIA_00015 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 388
No_of_seqs    219 out of 911
Neff          7.5 
Searched_HMMs 39220
Date          Sun May 22 13:17:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780124.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam10926 DUF2800 Protein of u 100.0       0       0  780.8  33.7  354    4-375     1-363 (363)
  2 TIGR03623 probable DNA repair   99.9   2E-23 5.1E-28  173.4  14.8  235    3-238   594-873 (874)
  3 TIGR02773 addB_Gpos ATP-depend  99.6 3.2E-14 8.1E-19  112.9  16.2  176    6-182   801-1041(1192)
  4 COG3857 AddB ATP-dependent nuc  99.6 6.7E-14 1.7E-18  110.8  14.7  171    6-178   751-973 (1108)
  5 COG2887 RecB family exonucleas  99.6 1.4E-13 3.6E-18  108.7  14.6  225    7-242     1-255 (269)
  6 TIGR02786 addB_alphas double-s  99.5   9E-13 2.3E-17  103.4  11.3  156    6-161   814-1005(1096)
  7 TIGR02784 addA_alphas double-s  99.4 1.1E-11 2.7E-16   96.3  12.4  166    6-176   993-1183(1190)
  8 TIGR00372 cas4 CRISPR-associat  99.3 1.6E-10 4.2E-15   88.5  13.6  186    7-238     1-205 (206)
  9 TIGR02774 rexB_recomb ATP-depe  99.0 7.1E-08 1.8E-12   71.2  17.0  292    5-337   760-1108(1116)
 10 PRK13909 putative recombinatio  99.0 8.5E-09 2.2E-13   77.3  11.8  134   34-178   766-904 (911)
 11 KOG1805 consensus               99.0 9.1E-08 2.3E-12   70.5  15.5  228    5-240   183-451 (1100)
 12 pfam01930 Cas_Cas4 Domain of u  98.9 3.8E-08 9.8E-13   73.0  12.4  158    9-238     2-161 (162)
 13 pfam09810 Morph_protein1 Defec  98.7 9.6E-06 2.4E-10   57.2  17.4  138    7-157    14-176 (329)
 14 TIGR03491 RecB family nuclease  98.6 4.6E-06 1.2E-10   59.3  15.2  193    7-243     1-205 (457)
 15 PHA00619 CRISPR-associated Cas  98.4 1.9E-05 4.9E-10   55.3  13.9  162   14-238    36-207 (210)
 16 COG1074 RecB ATP-dependent exo  98.4 1.5E-06 3.7E-11   62.6   7.2   47  112-158  1061-1118(1139)
 17 PHA01622 CRISPR-associated Cas  98.3 1.1E-05 2.8E-10   56.9  11.0  131   96-238    68-200 (204)
 18 COG1468 CRISPR-associated prot  98.3 4.3E-05 1.1E-09   52.9  13.2  169    5-239    14-188 (190)
 19 pfam06023 DUF911 Archaeal prot  98.3 5.2E-05 1.3E-09   52.4  13.2  204   17-238    54-289 (290)
 20 TIGR02785 addA_Gpos recombinat  98.1   1E-05 2.6E-10   57.0   7.4   52  109-160  1214-1277(1295)
 21 TIGR00609 recB exodeoxyribonuc  97.9 5.7E-05 1.5E-09   52.1   7.8   55  112-166  1207-1279(1324)
 22 COG2251 Predicted nuclease (Re  97.9  0.0013 3.3E-08   43.2  14.5  254    6-285     2-278 (474)
 23 PRK10876 recB exonuclease V su  97.8 7.3E-05 1.9E-09   51.4   6.2   15  228-242   549-563 (1181)
 24 pfam08696 Dna2 DNA replication  97.8 9.4E-05 2.4E-09   50.7   6.6   49    5-53     58-108 (209)
 25 COG4343 CRISPR-associated prot  97.1   0.012 3.1E-07   36.8  10.9  207   15-238    51-280 (281)
 26 TIGR01896 cas_AF1879 CRISPR-as  95.0    0.29 7.4E-06   27.8   9.8  122   99-238   164-295 (295)
 27 PRK09709 exonuclease VIII; Rev  92.5    0.83 2.1E-05   24.8  10.9   16  145-160   791-806 (877)
 28 TIGR00423 TIGR00423 conserved   86.1    0.66 1.7E-05   25.4   2.8   13  223-235    14-26  (331)
 29 KOG4760 consensus               84.5       3 7.8E-05   21.1   8.1   40   99-138   156-196 (365)
 30 pfam02477 Nairo_nucleo Nucleoc  80.8     1.1 2.9E-05   23.9   2.2   39  121-160    98-136 (442)
 31 COG1023 Gnd Predicted 6-phosph  75.0     6.1 0.00016   19.1   5.0   60  250-312   195-254 (300)
 32 pfam06250 DUF1016 Protein of u  68.3     8.4 0.00021   18.2   4.0   77   88-172   199-278 (320)
 33 COG1060 ThiH Thiamine biosynth  65.3     6.4 0.00016   18.9   2.9   53  269-321   293-351 (370)
 34 PRK06245 cofG FO synthase subu  64.7       9 0.00023   18.0   3.5   67  284-355   258-327 (336)
 35 pfam05565 Sipho_Gp157 Siphovir  61.4     7.9  0.0002   18.4   2.7   29  258-286    61-89  (162)
 36 TIGR03550 F420_cofG 7,8-dideme  59.2      13 0.00032   17.0   3.5   38  283-321   254-295 (322)
 37 PRK08445 hypothetical protein;  58.6     8.6 0.00022   18.1   2.5   16   34-49     17-32  (348)
 38 pfam00285 Citrate_synt Citrate  56.8      14 0.00035   16.7   4.1   51  257-318   218-268 (352)
 39 PRK05904 coproporphyrinogen II  56.8      14 0.00035   16.7   3.6   13   10-22      5-17  (353)
 40 PRK05927 hypothetical protein;  54.7      11 0.00029   17.3   2.6   13  351-363   305-317 (350)
 41 PRK10880 adenine DNA glycosyla  50.7      16 0.00041   16.3   2.9   37  203-245   180-216 (350)
 42 COG1194 MutY A/G-specific DNA   50.2      18 0.00045   16.1   4.2   52  189-246   164-222 (342)
 43 PRK12349 citrate synthase 3; P  49.6      18 0.00046   16.0   4.3   41  257-308   224-265 (365)
 44 cd06109 BsCS-I_like Bacillus s  47.1      20  0.0005   15.7   3.8   52  256-318   207-258 (349)
 45 COG0792 Predicted endonuclease  46.7      20 0.00051   15.7   3.9   43  113-155    32-79  (114)
 46 TIGR03551 F420_cofH 7,8-dideme  46.2      20 0.00051   15.7   2.8   13   35-47     16-28  (343)
 47 PRK06582 coproporphyrinogen II  45.8     6.5 0.00017   18.9   0.2   12  305-316   313-324 (390)
 48 PRK08444 hypothetical protein;  45.1      21 0.00054   15.5   3.9   13  351-363   307-319 (353)
 49 PRK09736 5-methylcytosine-spec  44.3      22 0.00055   15.5  11.0   66  115-180   244-313 (350)
 50 PRK06341 single-stranded DNA-b  43.6      13 0.00033   16.9   1.5   34  273-310    60-93  (165)
 51 COG5175 MOT2 Transcriptional r  43.5      15 0.00039   16.4   1.9   11  112-122   143-153 (480)
 52 cd06112 citrate_synt_like_1_1   42.2      23 0.00059   15.3   3.8   51  257-318   223-273 (373)
 53 PRK07360 FO synthase subunit 2  42.2      18 0.00045   16.0   2.0   34  330-364   308-341 (375)
 54 KOG1150 consensus               41.4      17 0.00043   16.2   1.8   14  358-371   139-152 (250)
 55 TIGR00872 gnd_rel 6-phosphoglu  41.2      16  0.0004   16.4   1.6   57  253-312   239-295 (341)
 56 KOG2672 consensus               40.7     8.6 0.00022   18.1   0.2   32  108-139   104-138 (360)
 57 PRK03298 hypothetical protein;  40.5      25 0.00063   15.1   4.3   59  110-177   131-190 (224)
 58 pfam07211 consensus             40.5      25 0.00063   15.1   6.6   54  272-326    55-114 (162)
 59 COG4950 Uncharacterized protei  40.0      10 0.00026   17.6   0.5   62  226-287    75-145 (193)
 60 PRK09058 coproporphyrinogen II  38.9      26 0.00067   14.9   3.5   11  125-135   209-219 (447)
 61 TIGR01979 sufS cysteine desulf  37.2      26 0.00065   15.0   2.2   95  144-274   306-408 (409)
 62 KOG0437 consensus               36.8      22 0.00056   15.4   1.8   59  226-284   841-914 (1080)
 63 PRK05926 hypothetical protein;  36.5      28 0.00073   14.7   2.9   13  351-363   330-342 (371)
 64 PRK08898 coproporphyrinogen II  36.2      21 0.00052   15.6   1.6   15  353-367   364-378 (393)
 65 PRK12351 methylcitrate synthas  35.3      30 0.00076   14.6   3.6   51  257-318   228-278 (377)
 66 pfam04577 DUF563 Protein of un  34.5      31 0.00078   14.5   2.5   31  291-322   210-240 (246)
 67 PRK13347 coproporphyrinogen II  33.9      31  0.0008   14.4   5.2   14  354-367   412-425 (453)
 68 pfam08011 DUF1703 Protein of u  33.3      32 0.00081   14.4   2.9   45  111-155    27-76  (101)
 69 TIGR01823 PabB-fungal para-ami  32.9      31 0.00078   14.5   2.0   73  224-307   632-705 (851)
 70 PRK06642 single-stranded DNA-b  32.7      21 0.00054   15.5   1.2   35  272-310    59-93  (152)
 71 COG0372 GltA Citrate synthase   32.2      33 0.00085   14.2   4.0   51  257-317   235-285 (390)
 72 cd06106 ScCit3_like Saccharomy  31.1      35 0.00088   14.1   3.4   56  256-318   273-331 (428)
 73 PRK09234 fbiC FO synthase; Rev  30.9      35 0.00089   14.1   4.7   19  217-235   533-551 (846)
 74 cd06110 BSuCS-II_like Bacillus  30.4      36 0.00091   14.0   4.0   51  257-318   219-269 (356)
 75 TIGR01793 cit_synth_euk citrat  30.1      35 0.00088   14.1   1.9   50  275-326   299-348 (430)
 76 COG1801 Uncharacterized conser  29.7      37 0.00093   14.0   6.7   32    4-35     47-79  (263)
 77 KOG0649 consensus               29.0      27 0.00069   14.8   1.2   25  123-147   177-202 (325)
 78 PRK08207 coproporphyrinogen II  28.6      38 0.00097   13.8   3.7   17  252-268   238-254 (497)
 79 TIGR01084 mutY A/G-specific ad  27.7      35  0.0009   14.1   1.6   38  204-247   191-228 (297)
 80 pfam09856 DUF2083 Predicted tr  27.0      34 0.00088   14.1   1.5   24  221-245   117-140 (156)
 81 PRK13627 carnitine operon prot  26.8      28 0.00071   14.7   1.0   21  353-373   174-194 (196)
 82 COG1637 Predicted nuclease of   26.0      42  0.0011   13.5   8.6   37  113-152   160-197 (253)
 83 cd06115 AthCS_per_like Arabido  25.1      44  0.0011   13.4   3.9   52  257-319   258-309 (410)
 84 PRK08173 DNA topoisomerase III  24.5      45  0.0012   13.4   2.4   32  327-363   766-797 (857)
 85 cd06118 citrate_synt_like_1 Ci  24.4      45  0.0012   13.4   3.6   46  265-318   224-269 (358)
 86 pfam01939 DUF91 Protein of unk  24.4      45  0.0012   13.4   5.0   59  111-177   133-192 (228)
 87 KOG2457 consensus               23.5      27 0.00068   14.9   0.4   23  222-244   290-314 (555)
 88 TIGR01311 glycerol_kin glycero  23.3      19 0.00047   15.9  -0.5   37  110-147   163-210 (518)
 89 TIGR00770 Dcu transporter, ana  23.2      29 0.00074   14.6   0.5   11   45-55     72-82  (447)
 90 COG2810 Predicted type IV rest  22.9      48  0.0012   13.2   3.6   73   85-163    32-105 (284)
 91 KOG3300 consensus               22.4      50  0.0013   13.1   3.0   33  267-299    80-112 (146)
 92 cd06111 DsCS_like Cold-active   22.2      50  0.0013   13.1   3.4   50  257-317   219-268 (362)
 93 TIGR02187 GlrX_arch Glutaredox  22.0      32 0.00082   14.3   0.5   21  225-249   156-176 (237)
 94 COG3894 Uncharacterized metal-  21.9      27 0.00069   14.8   0.1   24  125-148   177-200 (614)
 95 PRK04247 hypothetical protein;  21.6      51  0.0013   13.0   5.0   56  112-176   158-214 (250)
 96 cd06100 CCL_ACL-C Citryl-CoA l  21.5      52  0.0013   13.0   4.4   56  257-319    84-140 (227)
 97 cd06103 ScCS-like Saccharomyce  21.2      52  0.0013   12.9   4.5   55  257-318   274-331 (426)
 98 PRK12350 citrate synthase 2; P  21.1      53  0.0013   12.9   3.4   52  257-319   206-257 (352)
 99 PRK04424 fatty acid biosynthes  20.4      54  0.0014   12.8   4.2   19  267-285    47-65  (185)
100 pfam05813 Orthopox_F7 Orthopox  20.0      33 0.00085   14.2   0.3   14  226-239     7-21  (82)

No 1  
>pfam10926 DUF2800 Protein of unknown function (DUF2800). This is a family of uncharacterized proteins found in bacteria and viruses. Some members of this family are annotated as being Phi APSE P51-like proteins.
Probab=100.00  E-value=0  Score=780.78  Aligned_cols=354  Identities=36%  Similarity=0.536  Sum_probs=329.0

Q ss_pred             CCCCCCCCHHHHHCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             75618423677871832388621389998988999899999999997245765343220104564537757889999999
Q gi|254780124|r    4 HAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSM   83 (388)
Q Consensus         4 HA~LSpSs~~rwl~CP~s~~Le~~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v~~   83 (388)
                      ||+|||||+||||+||+|++|+.++||++|+||.+||++|+++|.+|++.++.....+...  ......++++|.++++.
T Consensus         1 HA~LS~Ssa~RWl~Cp~S~~l~~~~pd~~S~~A~eGT~aH~l~E~~L~~~l~~~~~~~~~~--~~~~~~~~~eM~~~~~~   78 (363)
T pfam10926         1 HALLSASSAHRWLNCPPSARLEEGFPDKSSPAAAEGTAAHELAELKLRKGLDAITKLGRNS--EADGEYVDEEMAEYVQE   78 (363)
T ss_pred             CCCCCCCCCHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC--CCCCEEECHHHHHHHHH
T ss_conf             9867845124655698549987249998987899758999999999985169632256555--66880508899999999


Q ss_pred             HHHHHHCCC---CCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             999985037---87368877553200044058999999998599799998113688767446687999999999984383
Q gi|254780124|r   84 VLAYVRTFS---GPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGD  160 (388)
Q Consensus        84 ~~~~~r~~~---~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~  160 (388)
                      |++++++.-   ....+.+|++++++.++|++|||+|+|++.+++|+|||||||+|++|+|++|+||++|||||++.|+.
T Consensus        79 Yvd~v~e~~~~~~~~~~~iEqrvd~s~~~p~~fGTaD~vii~~~~L~IiDlKyG~GV~V~A~~N~QL~lYALGAl~~~~~  158 (363)
T pfam10926        79 YVDFVREQIELAKDGVLLIEQRVDFSQIVPEGFGTGDVVIIADGVLHIIDLKYGKGVLVSAEGNPQLMLYALGALDEFDV  158 (363)
T ss_pred             HHHHHHHHHHCCCCCEEEEEEEECHHHCCCCCCCCEEEEEEECCEEEEEECCCCCCCEECCCCCHHHHHHHHHHHHHHCC
T ss_conf             99999999850679879999885223217887764128999388799998777877540246797899999999998166


Q ss_pred             CCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             56765138999998304887754302589889999999999999999857765304776678886666725764456201
Q gi|254780124|r  161 IFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPAL  240 (388)
Q Consensus       161 ~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~  240 (388)
                      +|+ +++|+|+|+|||+++   +|+|+++++||+.|++++       +++++..++.|++++.+|+|||||++|++||||
T Consensus       159 lyd-i~~V~mtI~QPR~~~---is~w~~s~~eL~~w~~~~-------~kp~A~~A~~g~gef~~G~~CrFCkak~~C~Ar  227 (363)
T pfam10926       159 LYD-FDTVRMTIFQPRLDN---ISTWEISAEELLEWAEEV-------VKPAAELAYAGDGEFKPGEHCRFCKAKATCRAR  227 (363)
T ss_pred             CCC-CCEEEEEEECCCCCC---CCEEEEEHHHHHHHHHHH-------HHHHHHHHHCCCCCCCCCCCCCCCCCHHHCHHH
T ss_conf             467-647999997457799---865887899999999999-------889999862799986789875306322228999


Q ss_pred             HHHHHHHHHCC---CC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHH
Q ss_conf             34678763022---00-599999999995438999999999999999997898478523205888786116989999999
Q gi|254780124|r  241 SRHVLLEATKD---PS-TNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELL  316 (388)
Q Consensus       241 a~~~l~~~~~~---p~-~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l  316 (388)
                      |++||.+++++   |+ .||++||++||.++++|++|++||++||++++++|++|||||||+|| |||+|+|+++|+++|
T Consensus       228 a~~~l~la~~df~~~~~~Ls~~ei~~il~~~~~l~~W~~dv~~~a~~~~~~G~~~pG~KlV~GR-s~Rkw~de~~~~~~l  306 (363)
T pfam10926       228 AQAVLNLAKYDFEDPTLDLTDEELAELLEKADLLEKWAKDVEAYALDEARNGKEVPGYKLVEGR-SNRKWTDEEAVAAAL  306 (363)
T ss_pred             HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCC-CCCCCCCHHHHHHHH
T ss_conf             9999988876215777689999999999714899999999999999999779987872661476-777647889999999


Q ss_pred             HHCCC--CCCHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHEECCCCCCEECCCCCCCHHH
Q ss_conf             86165--100000138988999974000242678987530015678982663078862000
Q gi|254780124|r  317 TSVLG--EEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTNKQ  375 (388)
Q Consensus       317 ~~~~~--~~~~~~~l~~~~~~ek~~~~~~~~~~~~~~l~~~i~k~~gkp~l~p~~d~~~~~  375 (388)
                      +.+|+  +++|+++|+|||+|||++|||+    |+++|++||+||+|||||||+||+||++
T Consensus       307 ~~~g~~~~~~y~~kli~pt~~ekllgkk~----f~ell~~li~k~~GkptLvp~sDkRpa~  363 (363)
T pfam10926       307 KAAGLKDEDIYKKKLISPTQAEKLLGKKK----FKELLGALIVKPPGKPTLVPESDKRPAL  363 (363)
T ss_pred             HHCCCCHHHCCCCCCCCHHHHHHHHCHHH----HHHHHHHHEECCCCCCEEEECCCCCCCC
T ss_conf             98699655421013689899998878788----9999761263689961782478888999


No 2  
>TIGR03623 probable DNA repair protein. Members of this protein family are bacterial proteins of about 900 amino acids in length. Members show extended homology to proteins in TIGR02786, the AddB protein of double-strand break repair via homologous recombination. Members of this family, therefore, may be DNA repair proteins.
Probab=99.91  E-value=2e-23  Score=173.43  Aligned_cols=235  Identities=14%  Similarity=0.073  Sum_probs=130.7

Q ss_pred             CCCCCCCCCHHHHHCCCHHHHHHC----CCCCCC---CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-----------
Q ss_conf             775618423677871832388621----389998---98899989999999999724576534322010-----------
Q gi|254780124|r    3 HHAFLSASSSHRWLKCPIAPTLES----KIPQTT---SIYASEGTFAHNLLAHCLEQGVDAETVSHQKL-----------   64 (388)
Q Consensus         3 ~HA~LSpSs~~rwl~CP~s~~Le~----~~pd~~---S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~-----------   64 (388)
                      .+...|+|-.+.++.||+.++++.    .-+++.   -.++.+||++|.++|.+++...+...+.....           
T Consensus       594 ~~~~gg~s~L~~qa~CPf~~f~~~rL~~~~~~~~~~gl~~~~rG~i~H~~Le~~~~~l~~~~~L~~l~~~~l~~~i~~a~  673 (874)
T TIGR03623       594 ERISGGTGLLKAQAACPFRAFAQHRLGARALEEPVDGLDALERGTLVHRVLELFWERLKNQAALNALDEAELEQLIAEAI  673 (874)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHH
T ss_conf             43567289999887092999999984998889866677977765999999999999825736454189999999999999


Q ss_pred             -----CC-CC----CC----HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEE-ECCEEEEE
Q ss_conf             -----45-64----53----775788999999999998503787368877553200044058999999998-59979999
Q gi|254780124|r   65 -----TF-EN----DT----RIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIF-NSTQWIIV  129 (388)
Q Consensus        65 -----~~-~~----~~----~~~~~e~~~~v~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~-~dg~l~Ii  129 (388)
                           .. ..    ..    ..-.+.+..++..+++.-+...+..++..|..++..+++..+.|+|||||. .||...||
T Consensus       674 ~~~l~~~~~~~~~~~~~~~~~le~~rl~~~l~~~L~~e~~r~pF~v~~~E~~~~~~~~~l~l~~riDRiD~~~dG~~~Ii  753 (874)
T TIGR03623       674 GEALAEEEARHSQTFPERFLELEQERLLQLLLEWLELERQRPPFEVVATEQNHSIEIGGLELKVRIDRIDRLADGRRLII  753 (874)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEEECCEEEEEEEECCCCCCCCCEEEE
T ss_conf             99999987643434548999999999999999999975567991388721564156757899768744301699988999


Q ss_pred             EEECCCCCCCCC----CCCHHHHHHHHHHHHH-CCCCCCCCCEEEEEEEEEECCCC--CCCCCCC--CCHHHHHHHHHHH
Q ss_conf             811368876744----6687999999999984-38356765138999998304887--7543025--8988999999999
Q gi|254780124|r  130 DFKYGAGVPVKA----ENNTQLMLYACGALHQ-YGDIFGRPEALTLTIIQPRVRTG--SPINEWV--ISADDLLEKAKEF  200 (388)
Q Consensus       130 DyKtGk~~~v~a----~~n~QL~lYALgA~~~-~~~~~~~~~~v~~~I~qpr~~~~--~~vs~~~--~s~eeL~~~~~~v  200 (388)
                      |||||+......    -.+|||+|||+..-.. -+..|..++.-...+...-.+..  +.+....  -.......|.+-+
T Consensus       754 DYKTG~~~~~~~~~~r~~~pQLplYa~~~~~~v~~i~~a~v~~~~~~~~gl~~~~~~~~~~~~~~~~~~~~~~~~w~~~~  833 (874)
T TIGR03623       754 DYKTGAPSVRDWLGERPVEPQLPLYALLAEDEVAGVAFAQVRAGKMKFSGLAEDKELIPGVKAFAKLKAEDEPDSWEEVL  833 (874)
T ss_pred             EECCCCCCCCHHHCCCCCCCCHHHHHHHCCCCCCHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHCCCCCCCCHHHHH
T ss_conf             82799998502221784445489999871587551021643157764100002443365554233421333446899999


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCC-C--CCCCCCCCCCCCCCC
Q ss_conf             9999999857765304776678-8--866667257644562
Q gi|254780124|r  201 KERGTLALSLKSKRAVSLEHYG-V--NDDSCRFCRAKVRCP  238 (388)
Q Consensus       201 ~~~a~~~~~~~a~~~~~~~~~~-~--~g~~CrfC~~k~~Cr  238 (388)
                      ..|-+ .+...+..-.+|.... |  +.+.|+||+|+.+||
T Consensus       834 ~~w~~-~L~~la~e~~~G~a~v~p~~~~~~C~yCd~~~lCR  873 (874)
T TIGR03623       834 ARWRQ-ELTALAEEFSAGYAAVDPKNSETDCRYCDLQPLCR  873 (874)
T ss_pred             HHHHH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHCCC
T ss_conf             99999-99999999968988878999877688798441037


No 3  
>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B; InterPro: IPR014140   DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in others. AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is not. This entry describes the ATP-dependent nuclease subunit B (AddB/RexB) protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous and functionally equivalent, merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function..
Probab=99.64  E-value=3.2e-14  Score=112.93  Aligned_cols=176  Identities=17%  Similarity=0.110  Sum_probs=98.6

Q ss_pred             CCCCCCHHHHHCCCHHHHHHCCC--CCCCC---HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHH-------
Q ss_conf             61842367787183238862138--99989---8899989999999999724576534322010456453775-------
Q gi|254780124|r    6 FLSASSSHRWLKCPIAPTLESKI--PQTTS---IYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIV-------   73 (388)
Q Consensus         6 ~LSpSs~~rwl~CP~s~~Le~~~--pd~~S---~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~-------   73 (388)
                      -+|-|..++|-.||++++...+.  .+...   +|-+.|.++|++++.. ...++.+.+.......+.-....       
T Consensus       801 ~~SVSRlE~Y~~CpF~hfa~yGLkl~ER~~Y~L~apDlG~~fH~~L~~I-s~~l~~e~Ldw~~L~k~~c~~~~~~ave~l  879 (1192)
T TIGR02773       801 QASVSRLEKYNACPFAHFAQYGLKLKERKIYKLEAPDLGQLFHEALKEI-SDELKEEELDWSDLTKEQCRALANEAVEEL  879 (1192)
T ss_pred             EEEEECCHHHCCCCHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHH-HHHHHHCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             2344010000178325565025320025525679963678999999999-999962378701147689999999999876


Q ss_pred             ----H------HHHHHHHHHHHHHH-----------HCCCCCCEEEEEEEEEEECC----C------------EEEEEEE
Q ss_conf             ----7------88999999999998-----------50378736887755320004----4------------0589999
Q gi|254780124|r   74 ----D------TEMASSVSMVLAYV-----------RTFSGPFLSETEVPLEPFTT----E------------PGATGTA  116 (388)
Q Consensus        74 ----~------~e~~~~v~~~~~~~-----------r~~~~~~~ve~E~~~~~~~~----~------------~~~~Gti  116 (388)
                          +      ...-.|++.-+..+           .......-+..|+.|-....    .            ..+.|+|
T Consensus       880 ~p~~q~~IL~SS~Ry~Y~~~rl~~i~~ra~~vl~Eq~K~S~F~P~g~E~~FG~~~~~se~~ppl~~~L~~G~~~~L~GRI  959 (1192)
T TIGR02773       880 VPKIQHEILLSSKRYRYVQKRLKRIVTRAVKVLSEQAKRSKFVPVGLELGFGFGGDNSEELPPLKLILKNGEELKLRGRI  959 (1192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCE
T ss_conf             34534776223467899999999999999999998753278721224541367989875678732232688767873210


Q ss_pred             EEEEEE---CCE-EEEEEEECCCCCC------CCCCCCHHHHHHHHHHHHH----C--CCCCCCCCEEEEEEEEEECCCC
Q ss_conf             999985---997-9999811368876------7446687999999999984----3--8356765138999998304887
Q gi|254780124|r  117 DILIFN---STQ-WIIVDFKYGAGVP------VKAENNTQLMLYACGALHQ----Y--GDIFGRPEALTLTIIQPRVRTG  180 (388)
Q Consensus       117 D~I~~~---dg~-l~IiDyKtGk~~~------v~a~~n~QL~lYALgA~~~----~--~~~~~~~~~v~~~I~qpr~~~~  180 (388)
                      ||||..   +++ |+|||||+|...+      |..--..||+.|--.++..    .  |.-..+.-...+.|+-|+....
T Consensus       960 DRvD~~e~e~~~ylRIIDYKSsnPsk~LDL~~VYYGl~LQmLtYLD~~l~~s~~~~~lg~~a~PaGvLYFhihdp~~~a~ 1039 (1192)
T TIGR02773       960 DRVDKAEKEDETYLRIIDYKSSNPSKKLDLTEVYYGLALQMLTYLDIVLTNSEKWLKLGNQAKPAGVLYFHIHDPIVSAK 1039 (1192)
T ss_pred             EEEEHCCCCCCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEC
T ss_conf             00211015898148888703788873543577666899999999999998589999710654776045566437233007


Q ss_pred             CC
Q ss_conf             75
Q gi|254780124|r  181 SP  182 (388)
Q Consensus       181 ~~  182 (388)
                      ..
T Consensus      1040 ~~ 1041 (1192)
T TIGR02773      1040 KD 1041 (1192)
T ss_pred             CC
T ss_conf             88


No 4  
>COG3857 AddB ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair]
Probab=99.60  E-value=6.7e-14  Score=110.80  Aligned_cols=171  Identities=20%  Similarity=0.145  Sum_probs=94.3

Q ss_pred             CCCCCCHHHHHCCCHHHHHHCCC--CCCCC---HHHHHHHHHHHHHHHHHHCCCCC----CCCC----CCCC--CCCCCC
Q ss_conf             61842367787183238862138--99989---88999899999999997245765----3432----2010--456453
Q gi|254780124|r    6 FLSASSSHRWLKCPIAPTLESKI--PQTTS---IYASEGTFAHNLLAHCLEQGVDA----ETVS----HQKL--TFENDT   70 (388)
Q Consensus         6 ~LSpSs~~rwl~CP~s~~Le~~~--pd~~S---~aA~~GT~~H~llE~~l~~~l~~----~~~~----~~~~--~~~~~~   70 (388)
                      -+|.|+..+|-+||.|++++.++  .+...   .+-..|.++|.+.|+.....-..    ....    ....  ..+...
T Consensus       751 ~~SVSrlE~f~~Cpf~yf~~ygL~Lker~~~~l~~~dlG~~fH~v~e~i~e~~~~~~~d~~~l~~~~~~~l~~~i~~~~~  830 (1108)
T COG3857         751 YLSVSRLEKFYRCPFSYFLEYGLGLKERKDIHLDARDLGNFFHRVFERISEEENLENQDWNFLNEEDCERLTQKIVEVLL  830 (1108)
T ss_pred             EEEHHHHHHHHCCCHHHHHHHHHCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             76518778887396799999862645000157786147899999999999864210688421358899999999999862


Q ss_pred             HHHH------HHHHHHHHHHHHH-HH----------CCCCCCEEEEEEEEEEEC-----------CCEEEEEEEEEEEEE
Q ss_conf             7757------8899999999999-85----------037873688775532000-----------440589999999985
Q gi|254780124|r   71 RIVD------TEMASSVSMVLAY-VR----------TFSGPFLSETEVPLEPFT-----------TEPGATGTADILIFN  122 (388)
Q Consensus        71 ~~~~------~e~~~~v~~~~~~-~r----------~~~~~~~ve~E~~~~~~~-----------~~~~~~GtiD~I~~~  122 (388)
                      +...      .-...|...-+.. ++          ...+...+..|..|....           ....+.|+||||+..
T Consensus       831 ~~~~~~il~ss~r~~y~~~kL~~Ivr~t~~iL~e~~~~~~f~pi~~E~~Fglk~~~~~~i~l~~g~~i~l~GrIDRID~~  910 (1108)
T COG3857         831 EKEQEQILLSSARYEYTLEKLEDIVRRTATILAEQAKFSDFEPIGEEASFGLKGLPPLTIGLPSGSEILLRGRIDRIDQL  910 (1108)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEECHHHHCCCCCCCCCCEECCCCCCEEEEEEEEEHHHHH
T ss_conf             78899998500777999999999999879999743455453020033314789987610117999869997433123332


Q ss_pred             --CCEEEEEEEECCCCCC----CCCCCCHHHHHHHHHHHHHCCCC---CCCCCEEEEEEEEEECC
Q ss_conf             --9979999811368876----74466879999999999843835---67651389999983048
Q gi|254780124|r  123 --STQWIIVDFKYGAGVP----VKAENNTQLMLYACGALHQYGDI---FGRPEALTLTIIQPRVR  178 (388)
Q Consensus       123 --dg~l~IiDyKtGk~~~----v~a~~n~QL~lYALgA~~~~~~~---~~~~~~v~~~I~qpr~~  178 (388)
                        ||-+.|||||+|...-    |..--++||+.|--++.+.....   +.  -...+.+.-|+..
T Consensus       911 ~~~~~l~IvDYKSsa~~f~l~~vYyGL~lQlmTYLdai~q~~~~~~~~p~--GalYfhm~eP~i~  973 (1108)
T COG3857         911 EKDGYLGIVDYKSSAHQFDLTDVYYGLSLQLMTYLDAIKQNAPEDDVKPG--GALYFHMHEPEIK  973 (1108)
T ss_pred             CCCCCEEEEEECCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCC--CEEEEEECCHHHH
T ss_conf             25881588872365211452432144128799999999874043115644--1478884385653


No 5  
>COG2887 RecB family exonuclease [DNA replication, recombination, and repair]
Probab=99.58  E-value=1.4e-13  Score=108.67  Aligned_cols=225  Identities=19%  Similarity=0.156  Sum_probs=115.2

Q ss_pred             CCCCCHHHHHCCCHHHHHHC--CCCCC-----CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC--------CCCCCCCH
Q ss_conf             18423677871832388621--38999-----89889998999999999972457653432201--------04564537
Q gi|254780124|r    7 LSASSSHRWLKCPIAPTLES--KIPQT-----TSIYASEGTFAHNLLAHCLEQGVDAETVSHQK--------LTFENDTR   71 (388)
Q Consensus         7 LSpSs~~rwl~CP~s~~Le~--~~pd~-----~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~--------~~~~~~~~   71 (388)
                      ||+|.+.+...||.+++...  .++..     ....+.+||+.|.+++.+... ..........        ...+....
T Consensus         1 ls~s~~~~l~r~p~~~~a~~i~~l~~~~~~~e~~~~~~~g~~~h~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~   79 (269)
T COG2887           1 LSVSRAEALRRCPYLFYARRILALPPLGTRAEEPEAAVRGTLLHAILEALVGE-RYHAAAAALAKLAWLLRKELAEAELP   79 (269)
T ss_pred             CCHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             96535756255851699998635377875100244243354799999988631-24432031677765555544310233


Q ss_pred             H-----HHHHHHHHHHHHH--HHHHCCCCCCE-EEEEEE-EEEECCC-EEEEEEEEEEEEE-CCEEEEEEEECCCCCC--
Q ss_conf             7-----5788999999999--99850378736-887755-3200044-0589999999985-9979999811368876--
Q gi|254780124|r   72 I-----VDTEMASSVSMVL--AYVRTFSGPFL-SETEVP-LEPFTTE-PGATGTADILIFN-STQWIIVDFKYGAGVP--  138 (388)
Q Consensus        72 ~-----~~~e~~~~v~~~~--~~~r~~~~~~~-ve~E~~-~~~~~~~-~~~~GtiD~I~~~-dg~l~IiDyKtGk~~~--  138 (388)
                      .     +...........+  .+-++..+... ...+.. ++..+.+ ..+.|+||||+++ +|++.|+|||||+.+.  
T Consensus        80 ~~~~~~~~~r~~~~~~~~~~~~~e~~r~~~~~~~~~e~~~~~~~i~~~i~l~G~aDRid~~~~g~i~ilDYKTG~~p~~a  159 (269)
T COG2887          80 GYTDAEWLDRLRARARAFLVYDWERERGTAFHAWLEEERGAELLIDGGIRLRGRADRIDKDADGELEILDYKTGKSPSAA  159 (269)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCEEEEECCCCEECCEEEECCCCCCCCEEEEEEECCCCCCHH
T ss_conf             34662034889986654534568761677333665552230467303402211430002478884689986348886243


Q ss_pred             -CCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             -7446687999999999984383567651389999983048877543025898899999999999999998577653047
Q gi|254780124|r  139 -VKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVS  217 (388)
Q Consensus       139 -v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~  217 (388)
                       ..+...+|+.+|+++.....-...   ..-.++....+  ..+.+.......+...     +.......|........+
T Consensus       160 ~~~~~~~~ql~~~~~~l~~~~~~~~---~p~~l~~v~~~--~~~~~~~~~~~~~~~~-----~~~~~~e~~~~l~~~~~~  229 (269)
T COG2887         160 RAPAAVSPQLALEALALIEGRFRGV---EPGQLRLVYLR--KSGRVGEAPDNREQLP-----QLALAREALAELAELLAG  229 (269)
T ss_pred             HCHHCCCHHHHHHHHHHHHCCCCCC---CCCCEEEEEEC--CCCCCCCCCHHHHHHH-----HHHHHHHHHHHHHHHCCC
T ss_conf             3211105346888998871455666---78872488865--7776677850666540-----057799999999875345


Q ss_pred             CCC-CCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             766-7888666672576445620134
Q gi|254780124|r  218 LEH-YGVNDDSCRFCRAKVRCPALSR  242 (388)
Q Consensus       218 ~~~-~~~~g~~CrfC~~k~~Cra~a~  242 (388)
                      .+. ......-|+||+....||.+..
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (269)
T COG2887         230 LEVRPRGYSSRCDLCPHQDLCPAYGG  255 (269)
T ss_pred             CCCCCCCCCHHCCCCCCCCCCCCCCC
T ss_conf             54344562100244444455776444


No 6  
>TIGR02786 addB_alphas double-strand break repair protein AddB; InterPro: IPR014153   AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage . More recently, a distantly related gene pair conserved in many alphaproteobacteria was shown also to function in double-stranded break repair in Rhizobium etli. This family consists of AddB proteins of alphaproteobacterial types..
Probab=99.47  E-value=9e-13  Score=103.39  Aligned_cols=156  Identities=21%  Similarity=0.149  Sum_probs=96.8

Q ss_pred             CCCCCCHHHHHCCCHHHHHHC-------CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC---------CCCC
Q ss_conf             618423677871832388621-------389998988999899999999997245765343220104---------5645
Q gi|254780124|r    6 FLSASSSHRWLKCPIAPTLES-------KIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLT---------FEND   69 (388)
Q Consensus         6 ~LSpSs~~rwl~CP~s~~Le~-------~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~---------~~~~   69 (388)
                      .+|-|-+++|+.=|++++-..       +=.+..-.||.+||++|.++|.+.+...+.-........         ....
T Consensus       814 ~~SVTeie~L~rDPYAiYAk~ILkL~pLdPl~~~p~AA~RG~liH~ile~f~~~~~~~~~~~a~~~L~~~~~~~l~~~~~  893 (1096)
T TIGR02786       814 KLSVTEIETLRRDPYAIYAKHILKLRPLDPLDRDPEAADRGTLIHDILERFVEEVADPLPADAADVLRKIGRKELASLNL  893 (1096)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             13553200356882177875521677677767883246632299999999987511467321799999999998674247


Q ss_pred             C----HHHHHHHHHHHHHHHHHHHCCCC---CCEEEEE--EEEEE------ECCCEEEEEEEEEEEE-ECCEEEEEEEEC
Q ss_conf             3----77578899999999999850378---7368877--55320------0044058999999998-599799998113
Q gi|254780124|r   70 T----RIVDTEMASSVSMVLAYVRTFSG---PFLSETE--VPLEP------FTTEPGATGTADILIF-NSTQWIIVDFKY  133 (388)
Q Consensus        70 ~----~~~~~e~~~~v~~~~~~~r~~~~---~~~ve~E--~~~~~------~~~~~~~~GtiD~I~~-~dg~l~IiDyKt  133 (388)
                      .    ..|-..+.....++.++.+++..   ....|.+  +.+..      -+.+++++|++|||++ .||++.|+||||
T Consensus       894 p~~~~a~W~pRf~~~A~~~~~wE~~Rr~~~~~~~~E~~~~~~~~~~~e~~~~~~g~tL~GrADRID~~~~G~~~I~DYKT  973 (1096)
T TIGR02786       894 PPEAEALWWPRFARIADWFADWERARRLDVRRIFAEARGRKELVGERELRAAIRGFTLSGRADRIDRTADGSAAILDYKT  973 (1096)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCEECCEEEEEEEEEEEECCCCCEEEEEECC
T ss_conf             87588863889999999999999874434321246300402576413440001452787787677636988479886246


Q ss_pred             CCCCC---CCCCCCHHHHHHHHHHHH-HCCCC
Q ss_conf             68876---744668799999999998-43835
Q gi|254780124|r  134 GAGVP---VKAENNTQLMLYACGALH-QYGDI  161 (388)
Q Consensus       134 Gk~~~---v~a~~n~QL~lYALgA~~-~~~~~  161 (388)
                      |..+.   |...-.+||.|=|..+.+ .|..+
T Consensus       974 G~pPS~kQv~~gl~pQLaLEaAll~~GaF~D~ 1005 (1096)
T TIGR02786       974 GAPPSGKQVRAGLSPQLALEAALLMRGAFKDI 1005 (1096)
T ss_pred             CCCCHHHHHHCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             88952898850362779999999981888577


No 7  
>TIGR02784 addA_alphas double-strand break repair helicase AddA; InterPro: IPR014151   AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the alphaproteobacteria and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species..
Probab=99.39  E-value=1.1e-11  Score=96.31  Aligned_cols=166  Identities=21%  Similarity=0.232  Sum_probs=92.2

Q ss_pred             CCCCCCHHHHHCCC--HHHH----HHCCCCCC--C-CHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCCC-CCC-HHH
Q ss_conf             61842367787183--2388----62138999--8-98899989999999999724576534-322010456-453-775
Q gi|254780124|r    6 FLSASSSHRWLKCP--IAPT----LESKIPQT--T-SIYASEGTFAHNLLAHCLEQGVDAET-VSHQKLTFE-NDT-RIV   73 (388)
Q Consensus         6 ~LSpSs~~rwl~CP--~s~~----Le~~~pd~--~-S~aA~~GT~~H~llE~~l~~~l~~~~-~~~~~~~~~-~~~-~~~   73 (388)
                      .||||++..-..-+  +..-    |+.-+-++  . .-+..+||++|.++|++=.-.-..+. ......... ..+ +--
T Consensus       993 pl~PS~~~~~i~~~~~~~~~~~~llSPvl~e~~~~~~~A~~RG~~lH~LLQ~LP~~~~~~R~~aA~ryL~~~~~~w~~a~ 1072 (1190)
T TIGR02784       993 PLAPSGLSAAIDSAEPGEAVRSTLLSPVLGEKTAARAFALLRGTLLHRLLQHLPDLPPEEREDAARRYLARSAADWPEAE 1072 (1190)
T ss_pred             CCCCCCCCCCCCCCCCCCCCHHHEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             42676665334467874101001010113787657689999999999999626798867779999998741024578688


Q ss_pred             HHHHHHHHHHHHHHHHC---CCCCCEEEEEE--EEEEECCC-EEEEEEEEEEEEECC--EEEEEEEECCCCCCCCCCC--
Q ss_conf             78899999999999850---37873688775--53200044-058999999998599--7999981136887674466--
Q gi|254780124|r   74 DTEMASSVSMVLAYVRT---FSGPFLSETEV--PLEPFTTE-PGATGTADILIFNST--QWIIVDFKYGAGVPVKAEN--  143 (388)
Q Consensus        74 ~~e~~~~v~~~~~~~r~---~~~~~~ve~E~--~~~~~~~~-~~~~GtiD~I~~~dg--~l~IiDyKtGk~~~v~a~~--  143 (388)
                      .+.+...|...++..+-   +.....-|+.+  .+...... ..+.|+|||+.|+++  ++.|+|||||+.+|..++.  
T Consensus      1073 R~~l~~~v~~vL~~p~~~~~F~~~SRAEV~i~G~l~~~g~~P~avSG~IDRL~v~~~kk~V~iVDyKTNr~~P~~~~e~p 1152 (1190)
T TIGR02784      1073 REKLLAAVLAVLDDPRLAPVFAEGSRAEVAIMGTLKEGGKQPLAVSGQIDRLAVDEDKKRVLIVDYKTNRPVPKTAEEVP 1152 (1190)
T ss_pred             HHHHHHHHHHHHCCCHHHHCCCCCCCEEEEEEEEECCCCCCCEEECCEEEEEEECCCCCEEEEEEECCCCCCCCCHHHHH
T ss_conf             99999999998416013200477773213454652358898516601688877737887899986216889888976521


Q ss_pred             ---CHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEE
Q ss_conf             ---879999999999843835676513899999830
Q gi|254780124|r  144 ---NTQLMLYACGALHQYGDIFGRPEALTLTIIQPR  176 (388)
Q Consensus       144 ---n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr  176 (388)
                         -.||.+|.-.....|+.     +.|+-.+....
T Consensus      1153 ~~Y~~QlA~Yr~~L~~lYPg-----~~v~a~Ll~Te 1183 (1190)
T TIGR02784      1153 PAYLRQLALYRALLRPLYPG-----RAVEAALLWTE 1183 (1190)
T ss_pred             HHHHHHHHHHHHHHHHHCCC-----CEEEEEEEECC
T ss_conf             89999999999998865889-----75999888627


No 8  
>TIGR00372 cas4 CRISPR-associated protein Cas4; InterPro: IPR013343   This entry consists of conserved proteins found in many prokaryotic genomes whose genes are associated with CRISPRs (Clustered, Regularly Interspaced Short Palidromic Repeats). The function of these proteins has not been experimentally determined, but computational analysis suggests that they be nucleases like RecB (IPR004586 from INTERPRO), functioning as part of a hypothetical DNA repair system , . .
Probab=99.29  E-value=1.6e-10  Score=88.54  Aligned_cols=186  Identities=19%  Similarity=0.227  Sum_probs=116.4

Q ss_pred             CCCCCHHHHHCCCHHHHHHC--CCCCCCC---HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             18423677871832388621--3899989---889998999999999972457653432201045645377578899999
Q gi|254780124|r    7 LSASSSHRWLKCPIAPTLES--KIPQTTS---IYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSV   81 (388)
Q Consensus         7 LSpSs~~rwl~CP~s~~Le~--~~pd~~S---~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v   81 (388)
                      +++|-+..|+-||..+++..  +.+..+.   +...+|+.+|+-++...+..+                           
T Consensus         1 ~~~s~v~~Y~yCPr~~~~~~~~~~~~~~~~~~~~m~~G~~~~~~~~~~~r~~~---------------------------   53 (206)
T TIGR00372         1 ITVSDVKEYLYCPRKLWLMKKGGSEEESEERKVSMEEGRLIHEEAERAVRKFL---------------------------   53 (206)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH---------------------------
T ss_conf             95667888875126999997525546754465012321466678765678887---------------------------


Q ss_pred             HHHHHHHHCCC-CCCEEEEEEEEEEECCCEEEEEEEEEEEEECC------EEEEEEEECCCCC---CCC--CCCCHHHHH
Q ss_conf             99999985037-87368877553200044058999999998599------7999981136887---674--466879999
Q gi|254780124|r   82 SMVLAYVRTFS-GPFLSETEVPLEPFTTEPGATGTADILIFNST------QWIIVDFKYGAGV---PVK--AENNTQLML  149 (388)
Q Consensus        82 ~~~~~~~r~~~-~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg------~l~IiDyKtGk~~---~v~--a~~n~QL~l  149 (388)
                             +... .....+.++.+.....+-.+.|.+|.+...++      ...++++|+|+..   ..+  ..+..||..
T Consensus        54 -------~~~~~~~~~~~~~v~l~~~~~g~~l~G~~D~~~~~~~~~~~g~~~~pvE~K~~~~~~~~~~~~~~~~~~Ql~a  126 (206)
T TIGR00372        54 -------KSLGFEEVKEEKEVELKSKKYGKGLKGVIDVVLEEDGEIGKGAEPVPVEVKSGKAKKRLLRERGLAHKLQLLA  126 (206)
T ss_pred             -------HHCCCCEEEEECCEEECCCCCCCEEECCEEEEEEECCCCCCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHH
T ss_conf             -------6403300222101453278546415401478986156444652012676762446677643565235789999


Q ss_pred             HHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC
Q ss_conf             999999843835676513899999830488775430258988999999999999999985776530477667--888666
Q gi|254780124|r  150 YACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHY--GVNDDS  227 (388)
Q Consensus       150 YALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~--~~~g~~  227 (388)
                      ||+.+...++.-...  .++..|+.+..+...  -.-.++.++ ...+..+...++.+++.       +..+  ...+..
T Consensus       127 Ya~~~~~~~~~~~~~--i~~~~~~y~~~~~~~--y~v~~~~~~-~k~~~~~~~~i~~~~~~-------~~~P~~~~~~~k  194 (206)
T TIGR00372       127 YALLLEERYGVEVSD--IVKGYLLYLEEGKKV--YEVEISEEL-RKKAVKLIEKIEKLLEG-------EKLPPPPKKSRK  194 (206)
T ss_pred             HHHHHHHHCCCCHHH--HHEEEEEEECCCEEE--EEEEECHHH-HHHHHHHHHHHHHHHHC-------CCCCCCCCCCCC
T ss_conf             999985521843006--002202563077389--998628248-99999999999999848-------815576888775


Q ss_pred             CCCCCCCCCCC
Q ss_conf             67257644562
Q gi|254780124|r  228 CRFCRAKVRCP  238 (388)
Q Consensus       228 CrfC~~k~~Cr  238 (388)
                      |.+|+|+.+|.
T Consensus       195 C~~C~y~~~C~  205 (206)
T TIGR00372       195 CKFCPYREICL  205 (206)
T ss_pred             CCCCCCCCCCC
T ss_conf             77755521258


No 9  
>TIGR02774 rexB_recomb ATP-dependent nuclease subunit B; InterPro: IPR014141   DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RecAB) in other. The AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is not. The partner may be designated AddB, as in Bacillus and in alphaproteobacteria, or RexB as in Streptococcus and Lactococcus. Note, however, that RexB proteins lack an N-terminal GxxGxGK[ST] ATP-binding motif found in Bacillus subtilis and related species, and this difference may be important. This entry represents RexB proteins as found in Streptococcus and Lactococcus..
Probab=99.03  E-value=7.1e-08  Score=71.21  Aligned_cols=292  Identities=15%  Similarity=0.104  Sum_probs=164.8

Q ss_pred             CCCCCCCHHHHHCCCHHHHHHC--CCCCCCCHH--H-HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC----C---CHH
Q ss_conf             5618423677871832388621--389998988--9-99899999999997245765343220104564----5---377
Q gi|254780124|r    5 AFLSASSSHRWLKCPIAPTLES--KIPQTTSIY--A-SEGTFAHNLLAHCLEQGVDAETVSHQKLTFEN----D---TRI   72 (388)
Q Consensus         5 A~LSpSs~~rwl~CP~s~~Le~--~~pd~~S~a--A-~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~----~---~~~   72 (388)
                      =+||+||.-.+=+=-.+|+|..  +..+..|..  + .-|+..|.+-|++|+..-..+.....+...-.    +   ...
T Consensus       760 L~LSaSaLT~FYnNqY~YFL~YVL~L~e~~siHPD~R~HG~YLHrvFEr~m~~~e~~e~Fd~~L~qaI~~t~QE~~F~~~  839 (1116)
T TIGR02774       760 LKLSASALTTFYNNQYKYFLKYVLGLEEEESIHPDARHHGNYLHRVFERLMKDQEGEESFDEKLNQAINETSQEEVFKAL  839 (1116)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             42201132135535578999874064422357888441343367999998416788961788999985202658899986


Q ss_pred             HHHHH-HHHHHH-HHHHHHCCC-----------------------------CCCE--EEE----EEEEEEECCCEEEEEE
Q ss_conf             57889-999999-999985037-----------------------------8736--887----7553200044058999
Q gi|254780124|r   73 VDTEM-ASSVSM-VLAYVRTFS-----------------------------GPFL--SET----EVPLEPFTTEPGATGT  115 (388)
Q Consensus        73 ~~~e~-~~~v~~-~~~~~r~~~-----------------------------~~~~--ve~----E~~~~~~~~~~~~~Gt  115 (388)
                      +.+.. ..+... ..|.+|+-.                             +...  .+.    ++.++-....+.++|.
T Consensus       840 Y~~~~Ea~yt~~iL~Diar~TA~ILr~n~~i~v~~~e~~qhylGdkdWqktPqalka~~~~~~~~L~~~nh~R~~~v~G~  919 (1116)
T TIGR02774       840 YQEDAEARYTLEILLDIARSTAPILRDNSAIQVIKEEEAQHYLGDKDWQKTPQALKALEGKDNFQLQIDNHGREIKVRGI  919 (1116)
T ss_pred             HCCCHHHHHHHHHHHHHHHHCCHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCEEEEEEE
T ss_conf             04364478869999998861222202585220477876421025401100057888606762056520565447898116


Q ss_pred             EEEEEE-EC-CEEEEEEEECCCCC---CCC-CCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCC
Q ss_conf             999998-59-97999981136887---674-4668799999999998438356765138999998304887754302589
Q gi|254780124|r  116 ADILIF-NS-TQWIIVDFKYGAGV---PVK-AENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVIS  189 (388)
Q Consensus       116 iD~I~~-~d-g~l~IiDyKtGk~~---~v~-a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s  189 (388)
                      |||||+ .+ |.|-|||||.|...   +.. --=||||+-|-.|.-+..+.-+...=-.-|+.+         ..++.++
T Consensus       920 iDRiDrLs~~~sLGvVDYKSS~~~F~~~~FYNGL~pQL~TYl~ALk~~~p~e~~~~~FGAmYLh---------mqeP~~~  990 (1116)
T TIGR02774       920 IDRIDRLSDGDSLGVVDYKSSAKKFDIAKFYNGLSPQLLTYLAALKRDKPSEIEAPIFGAMYLH---------MQEPKQD  990 (1116)
T ss_pred             EECEEECCCCCCEEEEECCCCCCCCCCHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHH---------HCCCCCH
T ss_conf             6000220578821456604676523641104787624799999984304444678755202123---------1485400


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC--CCCCCHHHHHHHHHHH
Q ss_conf             88999999999999999985776530477667888666672576445620134678763022--0059999999999543
Q gi|254780124|r  190 ADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKD--PSTNTTVELSKAYSSI  267 (388)
Q Consensus       190 ~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~a~~~l~~~~~~--p~~l~~~e~~~~l~~~  267 (388)
                      ...+......+    ..                   ..-+--+||++=-+.-..-|......  ....|++|+.=+|   
T Consensus       991 L~~~K~Ldn~~----v~-------------------~~~kal~Y~GLF~e~e~~~La~~~y~~K~~~ys~~El~~Ll--- 1044 (1116)
T TIGR02774       991 LVKLKNLDNDL----VE-------------------ELSKALKYKGLFSEKEKEHLAEGYYKSKANLYSDEELELLL--- 1044 (1116)
T ss_pred             HHHHHHHHHHH----HH-------------------HHHHHHCCCCCHHHHHHHHHHHHHHHCHHHCCCHHHHHHHH---
T ss_conf             88861023789----99-------------------99987304663147777775510011113206578999999---


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHCCCCHHHHHH
Q ss_conf             8999999999999999997898478523205888786116989999999861651000001389889999
Q gi|254780124|r  268 SLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQ  337 (388)
Q Consensus       268 ~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~~~~~~~~~~l~~~~~~ek  337 (388)
                          .+-+.+..-|.+.+++|+=.-.==--.|| |.--|.|+-+++.-..+ .++=.+-|.|+++...||
T Consensus      1045 ----~Yn~~LYkKAA~~I~~G~F~INPYT~dGr-sv~PygdQ~kaITGFEA-d~hm~~AR~L~kLpak~k 1108 (1116)
T TIGR02774      1045 ----DYNKYLYKKAAETILSGRFLINPYTEDGR-SVQPYGDQLKAITGFEA-DRHMGQARRLVKLPAKEK 1108 (1116)
T ss_pred             ----HHHHHHHHHHHHHHHCCCCCCCCCCCCCC-EECCHHHHHHHHHHHHH-HHHHHHHHHHCCCCHHHH
T ss_conf             ----99899999999886538740157478883-55742424343213245-457888403036870210


No 10 
>PRK13909 putative recombination protein RecB; Provisional
Probab=99.01  E-value=8.5e-09  Score=77.27  Aligned_cols=134  Identities=12%  Similarity=0.067  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC--C-CCCCHHHHHHHHHHHHHHHHH--HHCCCCCCEEEEEEEEEEECC
Q ss_conf             88999899999999997245765343220104--5-645377578899999999999--850378736887755320004
Q gi|254780124|r   34 IYASEGTFAHNLLAHCLEQGVDAETVSHQKLT--F-ENDTRIVDTEMASSVSMVLAY--VRTFSGPFLSETEVPLEPFTT  108 (388)
Q Consensus        34 ~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~--~-~~~~~~~~~e~~~~v~~~~~~--~r~~~~~~~ve~E~~~~~~~~  108 (388)
                      .+...||++|.++|..................  + ..-...-..++...+..++..  .+...+...+..|+.|..  .
T Consensus       766 ~~~~~G~~iH~~lE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~~~--~  843 (911)
T PRK13909        766 EAIYFGEALHYCLEMLYAFKEENLKVLKNLLKNKYGHFLSESDFEDLEKRLELLINNKEFQELIKDGKLLKEQALLF--N  843 (911)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHHCCCCEEEEEEEEE--C
T ss_conf             88989999999996586579867899999998743057998999999999999975966898717885568777865--8


Q ss_pred             CEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECC
Q ss_conf             4058999999998599799998113688767446687999999999984383567651389999983048
Q gi|254780124|r  109 EPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVR  178 (388)
Q Consensus       109 ~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~  178 (388)
                        +..|+|||+...++.+.|||||||+..  ...+.+||..|+-+....++.     +.|+.+++....+
T Consensus       844 --g~~~~ID~l~~~~~~~~IiDYKT~~~~--~~~y~~QL~~Y~~al~~i~~~-----k~v~~~l~yl~~~  904 (911)
T PRK13909        844 --GELKQIDLLLEKDEEYFVIDYKSSKKY--QDKHKAQVREYKEAISEIIPK-----KKVRAFIIYLLED  904 (911)
T ss_pred             --CEECCCEEEEEECCEEEEEECCCCCCC--CHHHHHHHHHHHHHHHHHCCC-----CEEEEEEEEECCC
T ss_conf             --806680489998999999973889998--568999999999999987799-----9468999995698


No 11 
>KOG1805 consensus
Probab=98.96  E-value=9.1e-08  Score=70.50  Aligned_cols=228  Identities=14%  Similarity=0.164  Sum_probs=130.8

Q ss_pred             CCCCCCCHHHHHCCCHHHHHHCCCC--CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC------------CCCCCCC
Q ss_conf             5618423677871832388621389--9989889998999999999972457653432201------------0456453
Q gi|254780124|r    5 AFLSASSSHRWLKCPIAPTLESKIP--QTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQK------------LTFENDT   70 (388)
Q Consensus         5 A~LSpSs~~rwl~CP~s~~Le~~~p--d~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~------------~~~~~~~   70 (388)
                      .+.|..+...=+-|+.+..|...|.  ++++.++..||++|++.+..+.+...+.......            .......
T Consensus       183 ~Lis~TtVasS~~C~Rr~VL~erfr~~n~~t~~mllGtIvHevfQ~al~qk~~~~~~~~~~~~~q~~~~~s~l~~~~~~~  262 (1100)
T KOG1805         183 DLISGTTVASSLFCLRRTVLNERFRSGNSHTKAMLLGTIVHEVFQKALIQKSFAVDELILQASLQISKYISELYALGVSE  262 (1100)
T ss_pred             CCCCCCCHHHCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCH
T ss_conf             52021000101455228888777415897225678889999999999870465055677778777788999999734677


Q ss_pred             HHHHHHHHHHHHHHHHHHHCC----------------CCCC-EEEEEEEEEEECCCE--EEEEEEEEEEE---ECC--EE
Q ss_conf             775788999999999998503----------------7873-688775532000440--58999999998---599--79
Q gi|254780124|r   71 RIVDTEMASSVSMVLAYVRTF----------------SGPF-LSETEVPLEPFTTEP--GATGTADILIF---NST--QW  126 (388)
Q Consensus        71 ~~~~~e~~~~v~~~~~~~r~~----------------~~~~-~ve~E~~~~~~~~~~--~~~GtiD~I~~---~dg--~l  126 (388)
                      ...+.+|.++...++.++-.+                .... .+---.+++-.+|.|  ++.|.||....   ..+  ++
T Consensus       263 ~~i~~el~~~l~~i~~~i~~f~~~~~s~~~~s~~~~~~~~~i~i~ev~DIEEniWsp~fGLKG~iDatv~v~v~~~~eti  342 (1100)
T KOG1805         263 DVIRNELEKYLPNICLWIEHFVHKPLSGSFPSKRGPLPSKSIQISEVIDIEENIWSPKFGLKGKIDATVRVKVEEGKETI  342 (1100)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHCCCCCCCCEEEEEEEEHHHHHCCCCCCCCCEEEEEEEEEECCCCCCC
T ss_conf             89999999999999999987511455577602027878876055321225655356213776400358999970475433


Q ss_pred             EEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99981136887674466879999999999843835676513899999830488775430258988999999999999999
Q gi|254780124|r  127 IIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTL  206 (388)
Q Consensus       127 ~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~  206 (388)
                      .=..+|||+..- +-++.-|..||+|.....++....     ...+++.+-+....+..-.....+|+...+++..+...
T Consensus       343 ~PLElKTGk~~~-sieh~~QvlLYtLl~seRy~~~~~-----~glL~YLk~~~~~~v~~~~~dlr~LL~~RN~lA~~~~h  416 (1100)
T KOG1805         343 MPLELKTGKSSS-SIEHVGQVLLYTLLLSERYEIPIL-----PGLLYYLKDGQLVEVPSKHSDLRGLLMLRNRLANDLVH  416 (1100)
T ss_pred             CCEEEECCCCCC-CHHHHHHHHHHHHHHHHHCCCCCC-----CCEEEEECCCCEEECCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             532430577666-367789999999998764067766-----65589961797754362147799999988887766655


Q ss_pred             HHHHHHHHHCCCCCCC---CCCCCCCCCCCCCCCCHH
Q ss_conf             9857765304776678---886666725764456201
Q gi|254780124|r  207 ALSLKSKRAVSLEHYG---VNDDSCRFCRAKVRCPAL  240 (388)
Q Consensus       207 ~~~~~a~~~~~~~~~~---~~g~~CrfC~~k~~Cra~  240 (388)
                      .....+.  ..+.+.+   ....-|..|.++..|-..
T Consensus       417 ~~~~~~s--~~~~~lpe~~~~d~~C~~cs~~~~c~~~  451 (1100)
T KOG1805         417 QEDVSAS--AQGGNLPEPILEDSSCDHCSHKTACSFF  451 (1100)
T ss_pred             HCCCCCC--CCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             3022322--3458998741246424267777788999


No 12 
>pfam01930 Cas_Cas4 Domain of unknown function DUF83. This domain has no known function. The domain contains three conserved cysteines at its C terminus.
Probab=98.93  E-value=3.8e-08  Score=72.98  Aligned_cols=158  Identities=17%  Similarity=0.151  Sum_probs=98.4

Q ss_pred             CCCHHHHHCCCHHHHHHC--CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             423677871832388621--389998988999899999999997245765343220104564537757889999999999
Q gi|254780124|r    9 ASSSHRWLKCPIAPTLES--KIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLA   86 (388)
Q Consensus         9 pSs~~rwl~CP~s~~Le~--~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~   86 (388)
                      .|-.+-|..||..++|..  ..++..+..+..|.++|+-.   ..                                   
T Consensus         2 g~~i~~y~~CpR~~wl~~~~~~~e~~~~~v~~Gr~lhE~~---y~-----------------------------------   43 (162)
T pfam01930         2 GTLINYYFICKRKLWLFSHGITMEENSETVEIGKLLHEES---YE-----------------------------------   43 (162)
T ss_pred             CCEEEEEEECHHHHHHHHCCCCCCCCHHHHHHHHHHHHHC---CC-----------------------------------
T ss_conf             7588688566679999973776013767887545751301---02-----------------------------------


Q ss_pred             HHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             98503787368877553200044058999999998599799998113688767446687999999999984383567651
Q gi|254780124|r   87 YVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPE  166 (388)
Q Consensus        87 ~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~  166 (388)
                        +..       .++.+       ...|.+|.|...+|.+.++.||.|+.. ..+ +..||..|++.+. ..+.     .
T Consensus        44 --r~~-------k~v~l-------~~~g~iD~v~~~~~~~~~vE~K~s~~~-~~a-~~~QL~~ya~~Le-~~g~-----~   99 (162)
T pfam01930        44 --REK-------KEVEI-------DGSIKIDFVTRRKGGLVVHEVKKSSKM-EEA-HRMQLLYYLYLLK-KRGI-----E   99 (162)
T ss_pred             --CCC-------CEEEE-------CCCEEEEEEEEECCEEEEEEEECCCCC-CHH-HHHHHHHHHHHHH-HCCC-----C
T ss_conf             --365-------16980-------574899999986995999998558999-808-9999999999999-8298-----6


Q ss_pred             EEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             389999983048877543025898899999999999999998577653047766788866667257644562
Q gi|254780124|r  167 ALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCP  238 (388)
Q Consensus       167 ~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cr  238 (388)
                      .....|+.+.......|   +++. ++.....++...+..++..    ...  +.+...+.|+.|.++..|-
T Consensus       100 v~~G~l~y~~~rrr~~V---~lt~-e~r~~~~~~i~~i~~i~~~----~~p--P~~~~~~~C~~Csy~~~C~  161 (162)
T pfam01930       100 AKEGVLHYPKERKREEV---ELTE-EDREELEEAIKEIEEIISS----EKP--PPPEKKKYCKKCAYREFCW  161 (162)
T ss_pred             CCCEEEEECCCCEEEEE---ECCH-HHHHHHHHHHHHHHHHHHC----CCC--CCCCCCCCCCCCCCHHHCC
T ss_conf             66179998568879999---8699-9999999999999999847----999--7999899798999741038


No 13 
>pfam09810 Morph_protein1 Defects in morphology protein 1, mitochondrial precursor. Members of this family of proteins are thought to be involved in cellular morphology, though little else is known about them.
Probab=98.65  E-value=9.6e-06  Score=57.21  Aligned_cols=138  Identities=19%  Similarity=0.135  Sum_probs=73.8

Q ss_pred             CCCCCHHHHHCCCHHHH--HHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             18423677871832388--6213899989889998999999999972457653432201045645377578899999999
Q gi|254780124|r    7 LSASSSHRWLKCPIAPT--LESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMV   84 (388)
Q Consensus         7 LSpSs~~rwl~CP~s~~--Le~~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~   84 (388)
                      ||-+-+-.=.=|=.++.  |....+-..++|+..||.+|..+|.-+.....-+.        ....+.+.-.+-+.++. 
T Consensus        14 LSVTdL~s~~WCElQ~~Y~L~~~g~~~~T~aMk~G~~~H~~LE~Evh~~V~vev--------~t~ED~~al~~~N~I~~-   84 (329)
T pfam09810        14 LSVTDLSSPAWCELQYEYTLTKFGRKERTPAMKRGIKIHEKLELEVHTTVPVEV--------TTKEDAWALRLLNIILG-   84 (329)
T ss_pred             EEECCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEC--------CCCHHHHHHHHHHHHHH-
T ss_conf             403102771024423330012478765568889879999998874367658754--------88207899999999999-


Q ss_pred             HHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEE-C-----------------CEEEEEEEECCCCCCCCCC----
Q ss_conf             99985037873688775532000440589999999985-9-----------------9799998113688767446----
Q gi|254780124|r   85 LAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFN-S-----------------TQWIIVDFKYGAGVPVKAE----  142 (388)
Q Consensus        85 ~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~-d-----------------g~l~IiDyKtGk~~~v~a~----  142 (388)
                      +...+..+  .  --|+.+-..+.+.-+.|.||-+-.. +                 ..+.|.|.||-....+..+    
T Consensus        85 L~tL~~~G--~--tREl~V~G~v~g~lv~GIIDeL~~~~~~~~~~~~~~~~~~~~~~~~l~i~DvKTR~~~~~Ps~~q~~  160 (329)
T pfam09810        85 LRTLREEG--I--TRELPVWGVVKGELLNGIIDELSYENPDPSLEETAASNYSSNAISELIISDTKTRRSKSLPSEAQKR  160 (329)
T ss_pred             HHHHHHCC--C--EEEEEEEEEECCEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHHHH
T ss_conf             99998548--4--4799999998899999996798974898430000013333467780699853057898898867762


Q ss_pred             -CCHHHHHHHHHHHHH
Q ss_conf             -687999999999984
Q gi|254780124|r  143 -NNTQLMLYACGALHQ  157 (388)
Q Consensus       143 -~n~QL~lYALgA~~~  157 (388)
                       ...|+++|-.....+
T Consensus       161 ~s~lQlmlY~~~l~~l  176 (329)
T pfam09810       161 PTLLQLMLYKYLLDDM  176 (329)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             4577999999999998


No 14 
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=98.63  E-value=4.6e-06  Score=59.32  Aligned_cols=193  Identities=15%  Similarity=0.112  Sum_probs=98.2

Q ss_pred             CCCCCHHHHHCCCHHHHHHCC----CCCCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             184236778718323886213----8999898899-98999999999972457653432201045645377578899999
Q gi|254780124|r    7 LSASSSHRWLKCPIAPTLESK----IPQTTSIYAS-EGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSV   81 (388)
Q Consensus         7 LSpSs~~rwl~CP~s~~Le~~----~pd~~S~aA~-~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v   81 (388)
                      ||+|-+..|+.|+.++.|...    .++.+...+. .-...++..+..+...                    ..    .+
T Consensus         1 is~~~L~~~~rC~rra~LD~~gd~~~~~~~~~~~~~l~~~~~~~~~~~l~~~--------------------~~----~~   56 (457)
T TIGR03491         1 ITDSDLLSFLRCRRRAWLDLYGDKQQKEAPPDFLLQLRQDKQAFVQLILEDP--------------------AA----RA   56 (457)
T ss_pred             CCHHHHHHHHCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCH--------------------HH----HH
T ss_conf             9878989885687088870258965589996778999999999999840473--------------------56----69


Q ss_pred             HHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECC-------EEEEEEEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             9999998503787368877553200044058999999998599-------799998113688767446687999999999
Q gi|254780124|r   82 SMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNST-------QWIIVDFKYGAGVPVKAENNTQLMLYACGA  154 (388)
Q Consensus        82 ~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg-------~l~IiDyKtGk~~~v~a~~n~QL~lYALgA  154 (388)
                      +.-++ +....-+.+...-+..+.. .+....|..|+++..+|       ...++|.|-|+.+  ..+.-.||.+|+..+
T Consensus        57 ~aT~~-am~~G~~~I~~~~L~~~~~-~~~~~~g~pdlLvk~~g~S~~G~~~Yepvd~Kl~r~~--k~~~~lqla~ys~lL  132 (457)
T TIGR03491        57 EAGLD-ACAAGADGIYGGRLKHDLP-QNLPHVSHPDLLVKDPGRSAWGDWAYEPVLIKLGKRP--KDEYRLVLAFHALLL  132 (457)
T ss_pred             HHHHH-HHHCCCCEEEEEEEECCCC-CCCCEEEECCEEEECCCCCCCCCCEEEEEEEEECCCC--CHHHHHHHHHHHHHH
T ss_conf             99999-9973886599999804667-7884047779899628988878832578776506779--899999999999999


Q ss_pred             HHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             98438356765138999998304887754302589889999999999999999857765304776678886666725764
Q gi|254780124|r  155 LHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAK  234 (388)
Q Consensus       155 ~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k  234 (388)
                      ....+..+.     .+.++.   ++..   ...+...++.....+   .....+..... ...++ .+++.++|.+|+++
T Consensus       133 ~~~Qg~~p~-----~~~lil---g~~~---~~~~~~~~~~~~~~~---~l~~~~~~l~~-~~~P~-~~~~r~~C~~C~w~  196 (457)
T TIGR03491       133 ESFQGVAPK-----KGLIIL---RDGN---SLKVELIKLLPQLRQ---DLADFLLTLNA-DLEPE-VFISRKKCTLCSWR  196 (457)
T ss_pred             HHHHCCCCC-----EEEEEE---CCCC---EEEEEHHHHHHHHHH---HHHHHHHHHCC-CCCCC-CCCCCCCCCCCCHH
T ss_conf             986378887-----599997---8996---799788998999999---99999998526-78998-89985548869638


Q ss_pred             CCCCHHHHH
Q ss_conf             456201346
Q gi|254780124|r  235 VRCPALSRH  243 (388)
Q Consensus       235 ~~Cra~a~~  243 (388)
                      ..|-+.++.
T Consensus       197 ~~C~~~~~~  205 (457)
T TIGR03491       197 KDCEAVAKE  205 (457)
T ss_pred             HHHHHHHHH
T ss_conf             898899884


No 15 
>PHA00619 CRISPR-associated Cas4-like protein
Probab=98.42  E-value=1.9e-05  Score=55.25  Aligned_cols=162  Identities=17%  Similarity=0.075  Sum_probs=83.0

Q ss_pred             HHHCCCHHHHHHC-CCCCCCC-HHH---HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             7871832388621-3899989-889---9989999999999724576534322010456453775788999999999998
Q gi|254780124|r   14 RWLKCPIAPTLES-KIPQTTS-IYA---SEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYV   88 (388)
Q Consensus        14 rwl~CP~s~~Le~-~~pd~~S-~aA---~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~~~   88 (388)
                      .-+.||.+.+|+. ..+.+.+ .++   ..|+..|..++..|+.. +-+.                              
T Consensus        36 els~ClRrs~l~~k~g~~k~~~~~~~rm~iG~~lH~~L~~iL~~~-gfE~------------------------------   84 (210)
T PHA00619         36 ELSRCLRRSWLMRKKGGVKLALEEAMKMHIGSGLHMRLQDILKKH-GFET------------------------------   84 (210)
T ss_pred             HHHHCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC-CCEE------------------------------
T ss_conf             644466799999865884741667766556388999999999857-9625------------------------------


Q ss_pred             HCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCC---CCC-CCCCHHHHHHHHHHHHHCCCCCCC
Q ss_conf             5037873688775532000440589999999985997999981136887---674-466879999999999843835676
Q gi|254780124|r   89 RTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGV---PVK-AENNTQLMLYACGALHQYGDIFGR  164 (388)
Q Consensus        89 r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~---~v~-a~~n~QL~lYALgA~~~~~~~~~~  164 (388)
                             .+.+|....   .+..+.|++|.+..  +.-.|+.+||....   .+. ..+-.||-.|--.|-...+.+|  
T Consensus        85 -------E~~Ver~~~---lGf~I~GRiDay~~--e~~~v~eiK~t~~~~l~~~~~~~hl~QLN~Yl~m~~a~~GyLy--  150 (210)
T PHA00619         85 -------ECRVERKTA---LGFEIVGRIDVYDK--EENTIYELKYTHMQDLDKGRLNNYLRQLNYYIEMANAMAGYLI--  150 (210)
T ss_pred             -------EEEEEEEEC---CCEEEEEEEEEECC--CCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCEEE--
T ss_conf             -------788998603---56599978874237--7775999985366667778707499999999999874257699--


Q ss_pred             CCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             5138999998304887754302589889999999-9999999998577653047766788866667257644562
Q gi|254780124|r  165 PEALTLTIIQPRVRTGSPINEWVISADDLLEKAK-EFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCP  238 (388)
Q Consensus       165 ~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~-~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cr  238 (388)
                             ++. +.+....|.         ..|.+ ++..++...-.+..+..+++ ....|+..|.||||..+|=
T Consensus       151 -------~V~-~dgr~eeik---------~~~~~t~l~~r~~af~i~~~E~~lpp-~K~~p~~~C~~CP~~~~Cw  207 (210)
T PHA00619        151 -------IVH-ADGRVEEIK---------RDWKETDLENRANAFGISVEENILPP-KKSKPDRECIECPFYNVCW  207 (210)
T ss_pred             -------EEE-CCCCHHHHH---------HHHHHHHHHHHHHHHCCCCHHCCCCC-CCCCCCCCEEECCCEEEEE
T ss_conf             -------998-489847776---------66443026665444002320202799-9899996102477101664


No 16 
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]
Probab=98.37  E-value=1.5e-06  Score=62.58  Aligned_cols=47  Identities=26%  Similarity=0.277  Sum_probs=22.0

Q ss_pred             EEEEEEEEEEECCEEEEEEEECCCCCCCCCC-----------CCHHHHHHHHHHHHHC
Q ss_conf             8999999998599799998113688767446-----------6879999999999843
Q gi|254780124|r  112 ATGTADILIFNSTQWIIVDFKYGAGVPVKAE-----------NNTQLMLYACGALHQY  158 (388)
Q Consensus       112 ~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~-----------~n~QL~lYALgA~~~~  158 (388)
                      +.|.||++.+.+|.+.|+||||.+-....+.           ...|+.+|+.++...+
T Consensus      1061 ~~G~IDl~f~~~~~~yivDYKTn~l~~~~~~y~~~~~~~~~~Y~~Q~~lY~~al~~~l 1118 (1139)
T COG1074        1061 LQGIIDLLFRHEGRYYILDYKTNRLGDDSAAYSPAEAMLKQRYDLQLQLYAEALHRIL 1118 (1139)
T ss_pred             EEEEEEEEEEECCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6778789999899999997048888985133114566666559999999999999983


No 17 
>PHA01622 CRISPR-associated Cas4-like protein
Probab=98.34  E-value=1.1e-05  Score=56.86  Aligned_cols=131  Identities=18%  Similarity=0.137  Sum_probs=81.2

Q ss_pred             EEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCC--CCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEE
Q ss_conf             688775532000440589999999985997999981136887--674466879999999999843835676513899999
Q gi|254780124|r   96 LSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGV--PVKAENNTQLMLYACGALHQYGDIFGRPEALTLTII  173 (388)
Q Consensus        96 ~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~--~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~  173 (388)
                      -.+.|++++....+..+.|++|.|-.++    ++.+||.+-.  .+...+-.|+.+|-++.    +....++..+.+ +|
T Consensus        68 nCetEv~Is~ei~GI~IsGRiD~iC~Nd----lIEiKTt~~~~~~p~~~Hl~Qv~vY~~l~----~~q~~~~~~iYi-VY  138 (204)
T PHA01622         68 NCQTEVEIKDEIEGIKISGRIDIVCNND----LLEIKTISYNYFQVKEYHLYQVALYYHIL----KKQNYQINNVYI-VY  138 (204)
T ss_pred             CCEEECCCCCCEEEEEEEEEEEEECCCC----EEEEEEEECCCCCCHHHHHHHHHHHHHHH----CCCCCCCCCEEE-EE
T ss_conf             7457323355401599972550102574----49999630203770588999999999997----347863342799-99


Q ss_pred             EEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             83048877543025898899999999999999998577653047766788866667257644562
Q gi|254780124|r  174 QPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCP  238 (388)
Q Consensus       174 qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cr  238 (388)
                      .-|.  ...|.++.++..-|...-.++.+++...-+...+....-- +....--|+.|.|+..|=
T Consensus       139 i~R~--~~eVkef~idesvLet~~~~~~~~i~~yk~~~~e~dyk~v-p~~d~~fCk~CeF~~kCi  200 (204)
T PHA01622        139 LNRN--TREVKQFKIDEKVLETYYQKVIEWIKKFKEYLKETDYKKV-PGVNNYICKSCEFKQKCI  200 (204)
T ss_pred             EECC--CCHHHHEEECHHHHHHHHHHHHHHHHHHHHHHHCCCHHCC-CCCCCEEECCCEEEEEEE
T ss_conf             9547--3255721204999999999999999999998520452017-787605751434421377


No 18 
>COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense    mechanisms]
Probab=98.30  E-value=4.3e-05  Score=52.94  Aligned_cols=169  Identities=17%  Similarity=0.168  Sum_probs=91.1

Q ss_pred             CCCCCCCHHHHHCCCHHHHH-HCCCCCCCCHHHH----HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             56184236778718323886-2138999898899----989999999999724576534322010456453775788999
Q gi|254780124|r    5 AFLSASSSHRWLKCPIAPTL-ESKIPQTTSIYAS----EGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMAS   79 (388)
Q Consensus         5 A~LSpSs~~rwl~CP~s~~L-e~~~pd~~S~aA~----~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e~~~   79 (388)
                      ..++.|-.+.++.||...++ ...+|..+++++.    .|..+|...+.+++...                         
T Consensus        14 ~~i~~~~v~~y~~Cprk~w~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~-------------------------   68 (190)
T COG1468          14 MRITGSDVNEYLYCPRKLWLFSRGGPEESPEVYSEGVELGKLIHEKLEKFLRDEK-------------------------   68 (190)
T ss_pred             EEECHHHHHHHHHCCHHHHHHHHCCCCCCCHHCCHHHHHHHHHHHHHHHHHCCCC-------------------------
T ss_conf             2412888788885679899998448656500025135555788888998851244-------------------------


Q ss_pred             HHHHHHHHHHCCCCCCEEEEE-EEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHC
Q ss_conf             999999998503787368877-5532000440589999999985997999981136887674466879999999999843
Q gi|254780124|r   80 SVSMVLAYVRTFSGPFLSETE-VPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQY  158 (388)
Q Consensus        80 ~v~~~~~~~r~~~~~~~ve~E-~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~  158 (388)
                                    .  +..+ .++    ..-.+.|..|...    ...++++|.|+...... +-.||.-|+. ....+
T Consensus        69 --------------~--v~l~~~~i----~~d~lk~~~~~~~----~~~~vEiK~~~~~~~~~-~~~Ql~~yly-l~e~~  122 (190)
T COG1468          69 --------------E--VELEGEWI----KIDFLKGRMDLEV----KDVVVEIKKSKKMEKAP-HKLQLAYYLY-LEEKL  122 (190)
T ss_pred             --------------C--CEECCEEE----EEEEECCCCEEEC----CCEEEEEECCCCCCCCH-HHHHHHHHHH-HHHHH
T ss_conf             --------------6--32312056----5542235300441----42138986576765354-7999999999-99860


Q ss_pred             CCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             83567651389999983048877543025898899999999999999998577653047766788866667257644562
Q gi|254780124|r  159 GDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCP  238 (388)
Q Consensus       159 ~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cr  238 (388)
                      +.     ..-...|+.|....   +-.-+++.+.... ...+...+...+...      .-+.+..+..|++|.|+.+|.
T Consensus       123 g~-----~v~~g~i~Y~~~~k---~~~Vei~~~~~e~-v~~~~~ei~~ile~~------~~p~~~~~~~C~~C~y~~iC~  187 (190)
T COG1468         123 GI-----AVAKGYIYYPKLKK---RVEVELTEELREE-VERVLKEIEEILEGG------KPPPPKKKKKCKKCAYREICF  187 (190)
T ss_pred             CC-----EEEEEEEEECCCCC---EEEEEECHHHHHH-HHHHHHHHHHHHHCC------CCCCCCCCCCCCCCCCCEECC
T ss_conf             92-----00368998525673---7999808999999-999999999998289------999999988699998633426


Q ss_pred             H
Q ss_conf             0
Q gi|254780124|r  239 A  239 (388)
Q Consensus       239 a  239 (388)
                      .
T Consensus       188 ~  188 (190)
T COG1468         188 P  188 (190)
T ss_pred             C
T ss_conf             7


No 19 
>pfam06023 DUF911 Archaeal protein of unknown function (DUF911). This family consists of several archaeal proteins of unknown function.
Probab=98.27  E-value=5.2e-05  Score=52.40  Aligned_cols=204  Identities=16%  Similarity=0.120  Sum_probs=100.5

Q ss_pred             CCCHH--HHHH--CCCCCCCCHHHHHHHHHHHHHHHHHHCCC----CCCCCCCCCCCCCCCCHHH-HHHHHHHHHH----
Q ss_conf             18323--8862--13899989889998999999999972457----6534322010456453775-7889999999----
Q gi|254780124|r   17 KCPIA--PTLE--SKIPQTTSIYASEGTFAHNLLAHCLEQGV----DAETVSHQKLTFENDTRIV-DTEMASSVSM----   83 (388)
Q Consensus        17 ~CP~s--~~Le--~~~pd~~S~aA~~GT~~H~llE~~l~~~l----~~~~~~~~~~~~~~~~~~~-~~e~~~~v~~----   83 (388)
                      .||-+  .+|.  .+..-+++....+|.++|++.-..++...    ................... .++....+..    
T Consensus        54 yCpT~RDvYLrrVlg~r~~~~~~~~~G~~iH~v~~~~~~~~kr~iysg~~~~~~~e~~~~~~~~~~~~e~~~~~~~l~~~  133 (290)
T pfam06023        54 YCPTGRDVYLKRVLGVRGEEGGPLVLGQAIHEAFAKAIEEVKSLIYSGEPPDSSLERSFMADEFGCPEDVREYAKALWKY  133 (290)
T ss_pred             CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             68985076888862645796354565189999999999999888744777755789987420225767888999999999


Q ss_pred             -------HHHHHHCC----CCC------CEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHH
Q ss_conf             -------99998503----787------3688775532000440589999999985997999981136887674466879
Q gi|254780124|r   84 -------VLAYVRTF----SGP------FLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQ  146 (388)
Q Consensus        84 -------~~~~~r~~----~~~------~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~Q  146 (388)
                             -++.+++.    ..+      .-+..|..++...-|.-..=++|..+..-+  .|+|.|+|..   +..+..|
T Consensus       134 ~a~r~~a~~~ev~a~~~~~~~dsl~~~aiPv~~E~~VDGs~LGLS~~l~~Da~i~~~~--~Vve~K~G~~---~~~H~La  208 (290)
T pfam06023       134 LASRVSAELSEVRSKFPKATEDSAAFRVIPVAVEVRVDGSPLGLSSYLRVDAFIPILP--LVVEMKVGSY---QERHELA  208 (290)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCHHHHEECCEEEEECCCCCCCCCCCCCCCCHHHCCCC--EEEEEECCCH---HHHHHHH
T ss_conf             9999987788887404457730233210445788235884136764404442320466--4899961754---5678988


Q ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             999999999843835676513899999830488775430-2589889999999999999999857765304776678886
Q gi|254780124|r  147 LMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINE-WVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVND  225 (388)
Q Consensus       147 L~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~-~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g  225 (388)
                      |.-|||+....++...|.--    .++- ..+....+.- ...=.++|..|-=+.+..++.++.       ++..+..+ 
T Consensus       209 lAGYALAiEs~~e~PVD~G~----lVyv-~~~~~v~~~~~~~~I~d~LR~~FLE~RDe~~~~v~-------~~~DPG~a-  275 (290)
T pfam06023       209 LAGYALAIESDLEIPVDYGL----LVYV-TFNGGVKIKARLVYISDSLRTEFLEERDRAIEIVD-------NGSDPGLA-  275 (290)
T ss_pred             HHHHHHHHHHHHCCCCEEEE----EEEE-EECCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHH-------CCCCCCCC-
T ss_conf             88899999887548714405----9999-97797589889998387899999998789999986-------27899998-


Q ss_pred             CCC-CCCCCCCCCC
Q ss_conf             666-7257644562
Q gi|254780124|r  226 DSC-RFCRAKVRCP  238 (388)
Q Consensus       226 ~~C-rfC~~k~~Cr  238 (388)
                      +.| .+|+|...|-
T Consensus       276 ~~C~~~CpF~~~Ch  289 (290)
T pfam06023       276 KKCPPTCPFYEVCH  289 (290)
T ss_pred             CCCCCCCCHHHHHC
T ss_conf             78998886477636


No 20 
>TIGR02785 addA_Gpos recombination helicase AddA; InterPro: IPR014152   AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the Firmicutes and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species..
Probab=98.14  E-value=1e-05  Score=56.99  Aligned_cols=52  Identities=17%  Similarity=0.095  Sum_probs=38.5

Q ss_pred             CEEEEEEEEEEEEECCEEEEEEEECCCCC---CCCCC---------CCHHHHHHHHHHHHHCCC
Q ss_conf             40589999999985997999981136887---67446---------687999999999984383
Q gi|254780124|r  109 EPGATGTADILIFNSTQWIIVDFKYGAGV---PVKAE---------NNTQLMLYACGALHQYGD  160 (388)
Q Consensus       109 ~~~~~GtiD~I~~~dg~l~IiDyKtGk~~---~v~a~---------~n~QL~lYALgA~~~~~~  160 (388)
                      ..-+.|+|||.+..+|.+..+||||=.--   +.+.+         ..-||.||+-+....+..
T Consensus      1214 ~~lv~GiIDgy~e~ed~~~L~DYKTD~v~gkf~~~~~~~~~~lk~rY~~Q~~LY~~AL~~~~~~ 1277 (1295)
T TIGR02785      1214 KILVQGIIDGYLESEDGLVLFDYKTDHVEGKFGSSFEGAINELKERYRGQLKLYEKALEEILKK 1277 (1295)
T ss_pred             EEEEEEEEEEEEEECCCEEEEEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             0788741222233368578987213334266788743312478888899999999999998389


No 21 
>TIGR00609 recB exodeoxyribonuclease V, beta subunit; InterPro: IPR004586   Exodeoxyribonuclease V, or RecBCD holoenzyme, (3.1.11.5 from EC) is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. The complex catalyses exonucleolytic cleavage in either the 5' to 3' or 3' to 5' direction to yield 5-phosphooligonucleotides in the presence of ATP. This is the beta subunit .; GO: 0005524 ATP binding, 0008854 exodeoxyribonuclease V activity, 0006281 DNA repair.
Probab=97.93  E-value=5.7e-05  Score=52.12  Aligned_cols=55  Identities=16%  Similarity=0.257  Sum_probs=38.0

Q ss_pred             EEEEEEEEEEECC-EEEEEEEECCC-CCCCCC-------------CCCHHHHHHHHHHHH---HCCCCCCCCC
Q ss_conf             8999999998599-79999811368-876744-------------668799999999998---4383567651
Q gi|254780124|r  112 ATGTADILIFNST-QWIIVDFKYGA-GVPVKA-------------ENNTQLMLYACGALH---QYGDIFGRPE  166 (388)
Q Consensus       112 ~~GtiD~I~~~dg-~l~IiDyKtGk-~~~v~a-------------~~n~QL~lYALgA~~---~~~~~~~~~~  166 (388)
                      +.|.||+|...+| ...||||||.. |.-.++             ..+.|=.||++|+..   ....-|+...
T Consensus      1207 L~GfiDLvF~~~g~~yyi~DYKsN~LG~~~s~Y~~~~l~~~i~~~~YdlQy~lY~~A~hryL~~r~~~y~~~~ 1279 (1324)
T TIGR00609      1207 LKGFIDLVFRHEGQRYYILDYKSNWLGKDASDYSPEALTEAILKERYDLQYLLYTLALHRYLKKRLKDYDYER 1279 (1324)
T ss_pred             HCCEEEEEEEECCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             1551689997089837998621064468821014799999999735817899999999999973588853554


No 22 
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=97.91  E-value=0.0013  Score=43.22  Aligned_cols=254  Identities=15%  Similarity=0.092  Sum_probs=116.3

Q ss_pred             CCCCCCHHHHHCCCHHHHHHC----CCCCCCCHHH---HHHHHHH--HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             618423677871832388621----3899989889---9989999--999999724576534322010456453775788
Q gi|254780124|r    6 FLSASSSHRWLKCPIAPTLES----KIPQTTSIYA---SEGTFAH--NLLAHCLEQGVDAETVSHQKLTFENDTRIVDTE   76 (388)
Q Consensus         6 ~LSpSs~~rwl~CP~s~~Le~----~~pd~~S~aA---~~GT~~H--~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e   76 (388)
                      +.|+|-.--+-.|+..+.|..    -.+++.+..-   ..-+.+|  ...+.-+  .+..+  ...+.....-.......
T Consensus         2 ~~~~s~l~~~~Rc~rr~~l~~~~~~~~r~~~~~~l~kl~~~~~~~~~~~~~~~f--~~~e~--~~~~~~i~~r~~~t~~~   77 (474)
T COG2251           2 LYSASDLLAYQRCQRRALLRTFDARLGRGPPVAVLLKLPQERAALINDHELKEF--QLREE--ETAKRLIIGRAAYTGTL   77 (474)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH--HHCCC--CCCCCEEECCCCCCHHH
T ss_conf             553889999874115678888777644585277887776789887668987663--11352--34531231443321788


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             99999999999850378736887755320004405899999999859979999811368876744668799999999998
Q gi|254780124|r   77 MASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALH  156 (388)
Q Consensus        77 ~~~~v~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~  156 (388)
                      |...+.....-+--....+. .....    ++..++.|..|.++.++++.+|+|-|.++..++.  ...|+..||+....
T Consensus        78 ~~~~a~~~~r~~L~~n~~~~-~~~~~----~~~~~~vg~pD~likdG~~yriv~~kl~k~pK~~--~~lq~a~ya~~La~  150 (474)
T COG2251          78 MAAGADEIFREVLIANRAPL-YQPVL----VGKIELVGFPDFLIKDGDVYRIVDAKLAKRPKLP--YRLQAAFYALLLAK  150 (474)
T ss_pred             HHHHHHHHHHHHHHHCCCCC-CCCCC----CCCCEEECCCCCEECCCCEEEEEECCCCCCCCCH--HHHHHHHHHHHHHH
T ss_conf             87557899999997277621-26410----0361460478524416867888522001376507--89999999999985


Q ss_pred             HCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCCCCCCCCC
Q ss_conf             4383567651389999983048877543025898899999999999999998577653047766-788866667257644
Q gi|254780124|r  157 QYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEH-YGVNDDSCRFCRAKV  235 (388)
Q Consensus       157 ~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~-~~~~g~~CrfC~~k~  235 (388)
                      ........+   .+.+.--+     .+   ..+ .+++.|...+..-........   ...... ..-....|+.|.|-.
T Consensus       151 ~g~~v~~~a---el~l~~~~-----~~---~y~-~~~l~~~~~v~~~l~~~~~~L---~~~~~~avr~~r~rC~~C~f~p  215 (474)
T COG2251         151 SGVPVAGNA---ELSLIGKV-----AV---PYS-VEDLIWLNDVQRFLDTIEEDL---HYEAKTAVRWIRARCTTCQFEP  215 (474)
T ss_pred             CCCCCCCCC---EEEECCCC-----CC---CCC-HHHHCCCHHHHHHHHHHHHHH---CCCCCCCCHHHHHHHHHHHCCH
T ss_conf             178667876---14402454-----56---662-233224157799999999972---3678875414664411854143


Q ss_pred             CCCHH--HHHHHHHH-HC---------CCCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             56201--34678763-02---------2005999999999-9543899999999999999999
Q gi|254780124|r  236 RCPAL--SRHVLLEA-TK---------DPSTNTTVELSKA-YSSISLIKSYVKACEDEMFKRL  285 (388)
Q Consensus       236 ~Cra~--a~~~l~~~-~~---------~p~~l~~~e~~~~-l~~~~~l~~w~~~v~~~a~~~~  285 (388)
                      .|-+.  ++..|.+. -.         +-...|.+++++. ++..+.+....+.+-..+-.|+
T Consensus       216 ~C~~~a~e~~~L~Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa  278 (474)
T COG2251         216 QCESEALEEDDLSLVPGITPSRYDVLEEVGITTIEDLADASLPILELVAGALTALAAQLVLQA  278 (474)
T ss_pred             HHHHHHHHCCCEECCCCCCHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             356888513551013799878899999738223999975255402566546777789999999


No 23 
>PRK10876 recB exonuclease V subunit beta; Provisional
Probab=97.78  E-value=7.3e-05  Score=51.41  Aligned_cols=15  Identities=13%  Similarity=0.031  Sum_probs=7.5

Q ss_pred             CCCCCCCCCCCHHHH
Q ss_conf             672576445620134
Q gi|254780124|r  228 CRFCRAKVRCPALSR  242 (388)
Q Consensus       228 CrfC~~k~~Cra~a~  242 (388)
                      ++|=+..-.||.+.+
T Consensus       549 l~~~DIaILvRs~~~  563 (1181)
T PRK10876        549 VRASDISVLVRSRQE  563 (1181)
T ss_pred             CCCCCEEEEECCCHH
T ss_conf             772116888446146


No 24 
>pfam08696 Dna2 DNA replication factor Dna2. Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways.
Probab=97.76  E-value=9.4e-05  Score=50.71  Aligned_cols=49  Identities=20%  Similarity=0.350  Sum_probs=43.4

Q ss_pred             CCCCCCCHHHHHCCCHHHHHHCCC--CCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             561842367787183238862138--9998988999899999999997245
Q gi|254780124|r    5 AFLSASSSHRWLKCPIAPTLESKI--PQTTSIYASEGTFAHNLLAHCLEQG   53 (388)
Q Consensus         5 A~LSpSs~~rwl~CP~s~~Le~~~--pd~~S~aA~~GT~~H~llE~~l~~~   53 (388)
                      -++|+++...++.||+++.|...+  +++.|.++..||.+|++.+..|+..
T Consensus        58 ~LIS~T~Va~s~~C~RraVL~~r~k~~~~~s~~ml~GtivHelfQ~~l~~~  108 (209)
T pfam08696        58 ILVSGTSVASSIQCPRRAVLQERFKGSGEPSKPMLIGTILHEIFQEALRAN  108 (209)
T ss_pred             CCEEEEEEECCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             425400440424366199999984468987534502343999999999739


No 25 
>COG4343 CRISPR-associated protein, RecB family exonuclease [Defense mechanisms]
Probab=97.13  E-value=0.012  Score=36.83  Aligned_cols=207  Identities=18%  Similarity=0.174  Sum_probs=95.6

Q ss_pred             HHCCCHH--HHHH--CCCCCCCCHHHHHHHHHHHHHHHHHHCC----CCCCCCCCCCCC--CCCCC---HHHHHHHHHHH
Q ss_conf             8718323--8862--1389998988999899999999997245----765343220104--56453---77578899999
Q gi|254780124|r   15 WLKCPIA--PTLE--SKIPQTTSIYASEGTFAHNLLAHCLEQG----VDAETVSHQKLT--FENDT---RIVDTEMASSV   81 (388)
Q Consensus        15 wl~CP~s--~~Le--~~~pd~~S~aA~~GT~~H~llE~~l~~~----l~~~~~~~~~~~--~~~~~---~~~~~e~~~~v   81 (388)
                      +-.||-+  .+|.  .++.-+.+....+|.++|++.-..++..    ...+.+......  .+...   ..+-.+..++.
T Consensus        51 y~yCpt~RdvYLk~Vlg~Rge~~~~l~lG~aIHea~~~~~~e~k~~~~sg~sp~~sv~~d~~~~~~~~~k~v~~~~~~~~  130 (281)
T COG4343          51 YGYCPTGRDVYLKRVLGVRGEGGFPLLLGAAIHEAFAKAIEEHKSLIYSGESPRESVLEDAREMANILAKRVWARLNEYC  130 (281)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             26788740668999862034677430367899999999999999875045683312067899987789888889887788


Q ss_pred             HH-HHHHH-----HCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEE--CCEEEEEEEECCCCCCCCCCCCHHHHHHHHH
Q ss_conf             99-99998-----5037873688775532000440589999999985--9979999811368876744668799999999
Q gi|254780124|r   82 SM-VLAYV-----RTFSGPFLSETEVPLEPFTTEPGATGTADILIFN--STQWIIVDFKYGAGVPVKAENNTQLMLYACG  153 (388)
Q Consensus        82 ~~-~~~~~-----r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~--dg~l~IiDyKtGk~~~v~a~~n~QL~lYALg  153 (388)
                      +. |....     ++.+....+..++-.++.+++-. -|-.|++..+  .+.-.|+++|+|.-   +..+..-|.-|||+
T Consensus       131 ~~~y~~~~~e~~~~tsds~~~~~~Pv~vE~~vDGsp-LGlS~lv~~D~~~~l~vv~elKvG~~---~e~hrLalAGYAlA  206 (281)
T COG4343         131 EISYMAVRSEKASRTSDSALSIGAPVLVEFNVDGSP-LGLSDLVRVDALVGLPVVVELKVGSY---REVHRLALAGYALA  206 (281)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEECCCEEEEECCCCCC-CCCCCEECCHHHCCCCEEEEEECCCH---HHHHHHHHHHHHHH
T ss_conf             999999998765422441013125358981478974-55533223001036765999941652---68999887446765


Q ss_pred             HHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCC
Q ss_conf             99843835676513899999830488775430258-9889999999999999999857765304776678886666-725
Q gi|254780124|r  154 ALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVI-SADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSC-RFC  231 (388)
Q Consensus       154 A~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~-s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~C-rfC  231 (388)
                      ....++...|.-     .+.+.+.+....++-.-+ -.+.|..|.=+.+.+++.++.       .+.++..+ +.| .-|
T Consensus       207 iEa~~eiPVD~G-----~li~vtvN~~vk~~~~l~~i~d~lRseFLe~RD~~~div~-------~g~DPG~a-~~C~~~C  273 (281)
T COG4343         207 IEADTEIPVDYG-----VLISVTVNSGVKIKARLVYIDDSLRSEFLEERDRVADIVE-------YGSDPGLA-KSCPSGC  273 (281)
T ss_pred             HHHHHCCCCCEE-----EEEEEEECCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHH-------CCCCCCCC-CCCCCCC
T ss_conf             324105873235-----7999997686068889997383788999987788999997-------38898999-8899998


Q ss_pred             CCCCCCC
Q ss_conf             7644562
Q gi|254780124|r  232 RAKVRCP  238 (388)
Q Consensus       232 ~~k~~Cr  238 (388)
                      +|...|-
T Consensus       274 ~F~~~Ch  280 (281)
T COG4343         274 PFYEVCH  280 (281)
T ss_pred             CHHHHCC
T ss_conf             4587518


No 26 
>TIGR01896 cas_AF1879 CRISPR-associated protein, Csa1 family; InterPro: IPR009260   This family consists of several archaeal strongly conserved proteins whose genes are associated with CRISPRs (Clustered, Regularly Interspaced Short Palidromic Repeats). The function of these proteins has not been experimentally determined, but computational analysis has suggested that they may function as nucleases in DNA repair, similar to RecB (IPR004586 from INTERPRO) . .
Probab=95.03  E-value=0.29  Score=27.76  Aligned_cols=122  Identities=21%  Similarity=0.224  Sum_probs=63.7

Q ss_pred             EEEEEEEECCCEEEEEEEEEEEEECC--EEE---EEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEE
Q ss_conf             77553200044058999999998599--799---9981136887674466879999999999843835676513899999
Q gi|254780124|r   99 TEVPLEPFTTEPGATGTADILIFNST--QWI---IVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTII  173 (388)
Q Consensus        99 ~E~~~~~~~~~~~~~GtiD~I~~~dg--~l~---IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~  173 (388)
                      +++-.++.++|-. -|=.|++.++..  .+-   |+..|+|+.   +..+.+=|+-||||....++...|.     ...+
T Consensus       164 iP~~~E~~VDGsp-lGLs~~l~Vda~~~~l~~dlVvE~K~G~~---~~~h~LALAGYALAiEa~~e~PvDy-----G~lv  234 (295)
T TIGR01896       164 IPVAVEYKVDGSP-LGLSDRLRVDALVLILPVDLVVEMKVGSY---QERHELALAGYALAIEADLEVPVDY-----GLLV  234 (295)
T ss_pred             CCEEEEECCCCCC-CCCCCCHHHHHHHHHCCCEEEEEEECCCH---HHHHHHHHHHHHHHHHHHHCCCEEE-----EEEE
T ss_conf             6557751268855-46420000654320178317998525873---5677777654588777630783213-----4789


Q ss_pred             EEECCCC--CCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCCCCCCCCC
Q ss_conf             8304887--754302--589889999999999999999857765304776678886666-7257644562
Q gi|254780124|r  174 QPRVRTG--SPINEW--VISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSC-RFCRAKVRCP  238 (388)
Q Consensus       174 qpr~~~~--~~vs~~--~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~~~g~~C-rfC~~k~~Cr  238 (388)
                      +-+..+.  .++...  .++ ++|+.   ++.+.=.+++..+..    +.++.-+ ..| .-|||..+|.
T Consensus       235 ~v~v~~gs~v~~~~~~~~i~-d~lR~---eFLe~RD~~~~~v~~----~~DPGlp-~~C~~~CPF~~~C~  295 (295)
T TIGR01896       235 YVNVNEGSKVEIKARLVYIS-DDLRR---EFLEERDEVIEIVES----GSDPGLP-PKCPPTCPFYEVCH  295 (295)
T ss_pred             EEEEECCCCEEEEEEEEEEC-HHHHH---HHHHHHHHHHHHHHC----CCCCCCC-CCCCCCCCCCCCCC
T ss_conf             99862787436899999847-47779---999988999999864----7742338-88834678435789


No 27 
>PRK09709 exonuclease VIII; Reviewed
Probab=92.54  E-value=0.83  Score=24.77  Aligned_cols=16  Identities=31%  Similarity=0.376  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHHHCCC
Q ss_conf             7999999999984383
Q gi|254780124|r  145 TQLMLYACGALHQYGD  160 (388)
Q Consensus       145 ~QL~lYALgA~~~~~~  160 (388)
                      .|-.+|.-|...++|.
T Consensus       791 vQaA~Y~dG~~~~tG~  806 (877)
T PRK09709        791 VQDAFYSDGYEAQFGV  806 (877)
T ss_pred             HHHHHHHCCHHHHCCC
T ss_conf             1456653320231277


No 28 
>TIGR00423 TIGR00423 conserved hypothetical protein TIGR00423; InterPro: IPR005244    This entry describes a family of conserved hypothetical proteins with no known function. .
Probab=86.15  E-value=0.66  Score=25.42  Aligned_cols=13  Identities=23%  Similarity=0.746  Sum_probs=6.0

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             8866667257644
Q gi|254780124|r  223 VNDDSCRFCRAKV  235 (388)
Q Consensus       223 ~~g~~CrfC~~k~  235 (388)
                      .+-.+|+||.|++
T Consensus        14 IC~~~C~FCAF~~   26 (331)
T TIGR00423        14 ICVGKCKFCAFRR   26 (331)
T ss_pred             HHHHCCCCCCCCC
T ss_conf             0232479633113


No 29 
>KOG4760 consensus
Probab=84.53  E-value=3  Score=21.06  Aligned_cols=40  Identities=15%  Similarity=0.051  Sum_probs=26.4

Q ss_pred             EEEEEEEECCCEEEEEEEEEEEEE-CCEEEEEEEECCCCCC
Q ss_conf             775532000440589999999985-9979999811368876
Q gi|254780124|r   99 TEVPLEPFTTEPGATGTADILIFN-STQWIIVDFKYGAGVP  138 (388)
Q Consensus        99 ~E~~~~~~~~~~~~~GtiD~I~~~-dg~l~IiDyKtGk~~~  138 (388)
                      .|..+-....++-++|.||-+-.+ =+++..+|+||-++..
T Consensus       156 refpv~ge~e~v~~vgVidE~~~~~f~~lel~~lktr~~~~  196 (365)
T KOG4760         156 REFPVFGEGEGVLLVGVIDELHYTAFGELELAELKTRRRPM  196 (365)
T ss_pred             CEEEECCCCCEEEEEEEEEEHHHHHHHHHHHHHHCCCCCCC
T ss_conf             02121024520489988754013555235776501224666


No 30 
>pfam02477 Nairo_nucleo Nucleocapsid N protein. The nucleoprotein of the ssRNA negative-strand Nairovirus is an internal part of the virus particle.
Probab=80.85  E-value=1.1  Score=23.86  Aligned_cols=39  Identities=26%  Similarity=0.152  Sum_probs=26.4

Q ss_pred             EECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             8599799998113688767446687999999999984383
Q gi|254780124|r  121 FNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGD  160 (388)
Q Consensus       121 ~~dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~  160 (388)
                      -+.+++-+.|-||+.- .++.-.-.||.-|+.+|+.....
T Consensus        98 kN~~~iK~WD~~Y~~L-~~evP~~EqL~~YQ~AAlkWRkD  136 (442)
T pfam02477        98 KNKDTIKLWDAKYMDL-KKEIPEPEQLVSYQQAALKWRKD  136 (442)
T ss_pred             CCCCCEEECHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             5986203201058887-40599989999999999987774


No 31 
>COG1023 Gnd Predicted 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]
Probab=75.01  E-value=6.1  Score=19.06  Aligned_cols=60  Identities=20%  Similarity=0.276  Sum_probs=44.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHH
Q ss_conf             220059999999999543899999999999999999789847852320588878611698999
Q gi|254780124|r  250 KDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRA  312 (388)
Q Consensus       250 ~~p~~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~  312 (388)
                      .-|..++-+++++++.+-+.|.+|+=++-+.|+..--+=.++.|+  |.+ +|--+||=+++.
T Consensus       195 ~s~fD~D~~~VA~vW~hGSVIrSWLldLt~~Af~~d~~L~q~~g~--v~d-SGEGrWTv~~al  254 (300)
T COG1023         195 NSPFDYDLEAVAEVWNHGSVIRSWLLDLTAEAFKKDPDLDQISGR--VSD-SGEGRWTVEEAL  254 (300)
T ss_pred             HCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCHHHHCCE--ECC-CCCCEEEHHHHH
T ss_conf             188887779999998276459999999999998548887776176--345-887506668777


No 32 
>pfam06250 DUF1016 Protein of unknown function (DUF1016). Family of uncharacterized proteins found in viruses, archaea and bacteria.
Probab=68.35  E-value=8.4  Score=18.17  Aligned_cols=77  Identities=17%  Similarity=0.210  Sum_probs=44.3

Q ss_pred             HHCCC-CCCEEEEEEEEEEECCCEEEEEEEEEEEEE--CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCC
Q ss_conf             85037-873688775532000440589999999985--997999981136887674466879999999999843835676
Q gi|254780124|r   88 VRTFS-GPFLSETEVPLEPFTTEPGATGTADILIFN--STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGR  164 (388)
Q Consensus        88 ~r~~~-~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~--dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~  164 (388)
                      ..+.+ +..+|....++....  -+.  .+|.|..+  =.-++|||+|+|+-.+   ++--||-+|-- ++...-..++.
T Consensus       199 LLELG~GFaFvgrQ~ri~v~~--~df--yiDLlFYh~~L~c~V~IELK~g~f~p---e~~GQl~~Yl~-~~d~~~k~~~d  270 (320)
T pfam06250       199 LLELGAGFAFVGRQKRIQVDD--EDF--YIDLLFYHRKLRCLVAVDLKIGKFKP---EYAGQMNFYLR-YLDKHEKQPGE  270 (320)
T ss_pred             HHHHCCCCEEEEEEEEEEECC--CEE--EHHHHHHHHHCCCEEEEEECCCCCCH---HHHHHHHHHHH-HHHHHHCCCCC
T ss_conf             998189816754557888779--323--40476663411413677641587677---88888999999-99888568889


Q ss_pred             CCEEEEEE
Q ss_conf             51389999
Q gi|254780124|r  165 PEALTLTI  172 (388)
Q Consensus       165 ~~~v~~~I  172 (388)
                      -.+|-+.+
T Consensus       271 NPtIGilL  278 (320)
T pfam06250       271 NPPIGIIL  278 (320)
T ss_pred             CCCEEEEE
T ss_conf             99800798


No 33 
>COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]
Probab=65.27  E-value=6.4  Score=18.92  Aligned_cols=53  Identities=9%  Similarity=0.123  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCC-CCCC----CEECCCCC-CCCCCCCHHHHHHHHHHCCC
Q ss_conf             999999999999999997898-4785----23205888-78611698999999986165
Q gi|254780124|r  269 LIKSYVKACEDEMFKRLNAGD-EIQG----YQLVEGRK-GNRSFKDINRAQELLTSVLG  321 (388)
Q Consensus       269 ~l~~w~~~v~~~a~~~~~~G~-~~~g----~Klv~gr~-~~r~~~d~~~~~~~l~~~~~  321 (388)
                      ....|+.+=..-+...+..|- .|-|    =++..... ....|...+.....++.+|.
T Consensus       293 ~~a~w~~~g~~~~~~~l~~GanD~ggt~~~E~v~~~a~~~~~~~~~~eel~~~i~~aG~  351 (370)
T COG1060         293 IQASWLRDGVILAQAALLSGANDLGGTGYEEKVNPAAGAFSGDWRSVEELAALIKEAGR  351 (370)
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf             41744103669999999828616767775534365555556789999999999998499


No 34 
>PRK06245 cofG FO synthase subunit 1; Reviewed
Probab=64.73  E-value=9  Score=17.98  Aligned_cols=67  Identities=25%  Similarity=0.316  Sum_probs=32.5

Q ss_pred             HHHCCC-CCCCCEECCC--CCCCCCCCCHHHHHHHHHHCCCCCCHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             997898-4785232058--88786116989999999861651000001389889999740002426789875300
Q gi|254780124|r  284 RLNAGD-EIQGYQLVEG--RKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQEL  355 (388)
Q Consensus       284 ~~~~G~-~~~g~Klv~g--r~~~r~~~d~~~~~~~l~~~~~~~~~~~~l~~~~~~ek~~~~~~~~~~~~~~l~~~  355 (388)
                      .+..|- .|-|--=|+-  -...+-|.+-+...+.+...|. .+-+|-.+-|.=.    .++=++++..+.+..+
T Consensus       258 ~L~~GanDlGGisp~t~d~vnpe~~wp~~~~l~~~~~~~g~-~l~~Rl~vyp~~~----~~~w~~~~~~~~~~~~  327 (336)
T PRK06245        258 FLEAGADDLGGISPVTKDEVNPEYPWPDIDELKEILEEAGW-QLKERLPVYPKYV----KEGWLSPRLQEKIERL  327 (336)
T ss_pred             HHHCCCCCCCCCCCCCCCEECCCCCCCCHHHHHHHHHHCCC-CCCCCCCCCHHHH----CCCCCCHHHHHHHHHH
T ss_conf             98678766788775766601889999899999999997599-6564368886675----1576698999999986


No 35 
>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=61.39  E-value=7.9  Score=18.35  Aligned_cols=29  Identities=17%  Similarity=0.194  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999995438999999999999999997
Q gi|254780124|r  258 VELSKAYSSISLIKSYVKACEDEMFKRLN  286 (388)
Q Consensus       258 ~e~~~~l~~~~~l~~w~~~v~~~a~~~~~  286 (388)
                      +|+-.+-.+..-+++-++.+++|....+.
T Consensus        61 ~e~krl~erkk~~enk~~~LK~yl~~~m~   89 (162)
T pfam05565        61 AEIKRLAERKKSIENKVKRLKDYLEEAME   89 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999899999999999999


No 36 
>TIGR03550 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit. This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria.
Probab=59.20  E-value=13  Score=16.99  Aligned_cols=38  Identities=13%  Similarity=0.098  Sum_probs=19.1

Q ss_pred             HHHHCCC-CCCCCE-EC--CCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             9997898-478523-20--588878611698999999986165
Q gi|254780124|r  283 KRLNAGD-EIQGYQ-LV--EGRKGNRSFKDINRAQELLTSVLG  321 (388)
Q Consensus       283 ~~~~~G~-~~~g~K-lv--~gr~~~r~~~d~~~~~~~l~~~~~  321 (388)
                      ..+..|- .+-|-- +.  .+ ++.+.|...+.......++|+
T Consensus       254 ~aL~~GanDlGG~~~~~~~~v-~~~~~~~~~~el~~~i~~aG~  295 (322)
T TIGR03550       254 LLLDAGIDDWGGVSPVTPDHV-NPEAPWPEIDELARATEEAGF  295 (322)
T ss_pred             HHHHCCCCCCCCCCCCCHHHC-CCCCCCCCHHHHHHHHHHCCC
T ss_conf             999679977888771427544-888999999999999998499


No 37 
>PRK08445 hypothetical protein; Provisional
Probab=58.55  E-value=8.6  Score=18.10  Aligned_cols=16  Identities=13%  Similarity=-0.056  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             8899989999999999
Q gi|254780124|r   34 IYASEGTFAHNLLAHC   49 (388)
Q Consensus        34 ~aA~~GT~~H~llE~~   49 (388)
                      +-...|.+|+.+-+..
T Consensus        17 dl~~L~~~A~~~R~~~   32 (348)
T PRK08445         17 PLKELGQMALARKQEL   32 (348)
T ss_pred             CHHHHHHHHHHHHHHH
T ss_conf             9999999999999997


No 38 
>pfam00285 Citrate_synt Citrate synthase.
Probab=56.84  E-value=14  Score=16.74  Aligned_cols=51  Identities=22%  Similarity=0.421  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             99999999543899999999999999999789847852320588878611698999999986
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      ++++.+.|..+   .+ .++++.|+.+.+.+|+.+|||       |.|.|++.|-=+..|+.
T Consensus       218 n~~v~~ml~~i---~~-~~~~~~~i~~~l~~~~~i~GF-------GHrvYk~~DPRa~~l~~  268 (352)
T pfam00285       218 NEAVLEMLEEI---GS-PENVEEYIEKALDKGERLMGF-------GHRVYKTYDPRARILKK  268 (352)
T ss_pred             HHHHHHHHHHH---CC-CHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH
T ss_conf             89999999995---58-166899999998468977678-------97668889956999999


No 39 
>PRK05904 coproporphyrinogen III oxidase; Provisional
Probab=56.76  E-value=14  Score=16.73  Aligned_cols=13  Identities=15%  Similarity=0.534  Sum_probs=5.2

Q ss_pred             CCHHHHHCCCHHH
Q ss_conf             2367787183238
Q gi|254780124|r   10 SSSHRWLKCPIAP   22 (388)
Q Consensus        10 Ss~~rwl~CP~s~   22 (388)
                      ...+-|++=|...
T Consensus         5 k~~~LYIHIPFC~   17 (353)
T PRK05904          5 KTKHLYIHIPFCQ   17 (353)
T ss_pred             CCCEEEEEECCCC
T ss_conf             8666999808998


No 40 
>PRK05927 hypothetical protein; Provisional
Probab=54.66  E-value=11  Score=17.34  Aligned_cols=13  Identities=23%  Similarity=0.248  Sum_probs=6.3

Q ss_pred             HHHHHEECCCCCC
Q ss_conf             7530015678982
Q gi|254780124|r  351 ELQELITRGDGKP  363 (388)
Q Consensus       351 ~l~~~i~k~~gkp  363 (388)
                      ++.+-|.+..|..
T Consensus       305 ~~eE~I~~aaG~~  317 (350)
T PRK05927        305 ILDESVHKCTGWD  317 (350)
T ss_pred             CEEEEEECCCCCC
T ss_conf             3000464322899


No 41 
>PRK10880 adenine DNA glycosylase; Provisional
Probab=50.67  E-value=16  Score=16.31  Aligned_cols=37  Identities=16%  Similarity=0.315  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             9999985776530477667888666672576445620134678
Q gi|254780124|r  203 RGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVL  245 (388)
Q Consensus       203 ~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~a~~~l  245 (388)
                      ..+.+++..+..+      .+....|.-||.+..|.|.....-
T Consensus       180 ~nQAlMDLGA~vC------tp~~P~C~~CPl~~~C~A~~~~~~  216 (350)
T PRK10880        180 FNQAMMDLGAMVC------TRSKPKCELCPLQNGCIAAANHSW  216 (350)
T ss_pred             HHHHHHHHHHHHC------CCCCCCCCCCCCCCCCHHHHCCCH
T ss_conf             9999999734102------799998788988220646427985


No 42 
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=50.19  E-value=18  Score=16.05  Aligned_cols=52  Identities=15%  Similarity=0.286  Sum_probs=32.8

Q ss_pred             CHHHHHHHHHH-------HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             98899999999-------99999999857765304776678886666725764456201346787
Q gi|254780124|r  189 SADDLLEKAKE-------FKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLL  246 (388)
Q Consensus       189 s~eeL~~~~~~-------v~~~a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~a~~~l~  246 (388)
                      +..++...++.       .....+.++...|..+.      +....|.-||++..|.|..+.+..
T Consensus       164 ~~~~~~~~~~~ll~p~~~~~~fnqammdlGA~ICt------~~~P~C~~CPl~~~c~a~~~g~~~  222 (342)
T COG1194         164 TKKELWELAEQLLTPDRRPGDFNQAMMDLGATICT------AKKPKCSLCPLRDNCAAYRNGTPE  222 (342)
T ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHC------CCCCCCCCCCCHHHHHHHHCCCCC
T ss_conf             05899999997448988767999999986367615------899987739466889999819964


No 43 
>PRK12349 citrate synthase 3; Provisional
Probab=49.60  E-value=18  Score=15.99  Aligned_cols=41  Identities=22%  Similarity=0.359  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCC-CC
Q ss_conf             99999999543899999999999999999789847852320588878611-69
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSF-KD  308 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~-~d  308 (388)
                      ++.+.+.|   +.+.+ .+++++|+.+.+.+|+.++||       |.|.| +.
T Consensus       224 ne~v~~ml---~ei~~-~~~~~~~i~~~l~~~~~i~GF-------GHrVY~k~  265 (365)
T PRK12349        224 NEAVMYML---LEAGT-VEKFEELLQKKLYNKEKIMGF-------GHRVYMKK  265 (365)
T ss_pred             HHHHHHHH---HHHCC-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCC
T ss_conf             89999999---98288-877999999987179961157-------87555788


No 44 
>cd06109 BsCS-I_like Bacillus subtilis (Bs) citrate synthase CS-I_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-I, one of two CS isozymes in the gram-positive B. subtilis. The majority of CS activity in B. subtilis is provided by the other isozyme, BsCS-II (not included in this group). BsCS-
Probab=47.11  E-value=20  Score=15.74  Aligned_cols=52  Identities=15%  Similarity=0.342  Sum_probs=35.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             999999999543899999999999999999789847852320588878611698999999986
Q gi|254780124|r  256 TTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       256 ~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      -++++.+.+..+.   . .+++++|..+.+.+|+.+|||       |.|.|++.|-=+..|++
T Consensus       207 A~~~v~~~l~ei~---~-~~~~~~~i~~~l~~~~~i~Gf-------GHrvY~~~DPRa~~l~~  258 (349)
T cd06109         207 APGPVLDMLDAIG---T-PENAEAWLREALARGERLMGF-------GHRVYRVRDPRADVLKA  258 (349)
T ss_pred             HHHHHHHHHHHHC---C-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH
T ss_conf             6799999999958---8-346999999998357875378-------98878999944999999


No 45 
>COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=46.68  E-value=20  Score=15.70  Aligned_cols=43  Identities=19%  Similarity=0.241  Sum_probs=31.8

Q ss_pred             EEEEEEEEEECCEEEEEEEECCCCCC----CC-CCCCHHHHHHHHHHH
Q ss_conf             99999999859979999811368876----74-466879999999999
Q gi|254780124|r  113 TGTADILIFNSTQWIIVDFKYGAGVP----VK-AENNTQLMLYACGAL  155 (388)
Q Consensus       113 ~GtiD~I~~~dg~l~IiDyKtGk~~~----v~-a~~n~QL~lYALgA~  155 (388)
                      +|-||.|-.++++++.|.-||.++..    .. .....|.++...+-+
T Consensus        32 ~GEIDlIa~~~~~ivFVEVK~R~~~~~g~a~~aV~~~K~~ki~~aA~~   79 (114)
T COG0792          32 YGEIDLIARDGDTVVFVEVKYRRNDLYGGAAEAVTPRKQRKLRRAARL   79 (114)
T ss_pred             CCCEEEEEECCCEEEEEEEEEECCCCCCCHHHHCCHHHHHHHHHHHHH
T ss_conf             874689996599899999974126776666774899999999999999


No 46 
>TIGR03551 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit. This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases.
Probab=46.21  E-value=20  Score=15.67  Aligned_cols=13  Identities=15%  Similarity=-0.084  Sum_probs=5.8

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             8999899999999
Q gi|254780124|r   35 YASEGTFAHNLLA   47 (388)
Q Consensus        35 aA~~GT~~H~llE   47 (388)
                      -...|.+|+.+=+
T Consensus        16 l~~L~~~A~~vR~   28 (343)
T TIGR03551        16 LFELFRLADELRR   28 (343)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999999


No 47 
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=45.79  E-value=6.5  Score=18.91  Aligned_cols=12  Identities=17%  Similarity=0.293  Sum_probs=6.1

Q ss_pred             CCCCHHHHHHHH
Q ss_conf             116989999999
Q gi|254780124|r  305 SFKDINRAQELL  316 (388)
Q Consensus       305 ~~~d~~~~~~~l  316 (388)
                      +.++++...+.+
T Consensus       313 ~Ls~~d~~~e~i  324 (390)
T PRK06582        313 KLTHQEIIEEIL  324 (390)
T ss_pred             CCCHHHHHHHHH
T ss_conf             189889999999


No 48 
>PRK08444 hypothetical protein; Provisional
Probab=45.12  E-value=21  Score=15.55  Aligned_cols=13  Identities=23%  Similarity=0.184  Sum_probs=5.8

Q ss_pred             HHHHHEECCCCCC
Q ss_conf             7530015678982
Q gi|254780124|r  351 ELQELITRGDGKP  363 (388)
Q Consensus       351 ~l~~~i~k~~gkp  363 (388)
                      ++.+-|.+..|.+
T Consensus       307 ~~eE~i~~~aGa~  319 (353)
T PRK08444        307 IEKESIQSAAGAK  319 (353)
T ss_pred             CCCCCEECCCCCC
T ss_conf             5545244212589


No 49 
>PRK09736 5-methylcytosine-specific restriction enzyme subunit McrC; Provisional
Probab=44.27  E-value=22  Score=15.46  Aligned_cols=66  Identities=17%  Similarity=0.170  Sum_probs=34.5

Q ss_pred             EEEEEEEECCEEEEEEEECCCCCCCCC---CCCHHHHHHHHHHHHHC-CCCCCCCCEEEEEEEEEECCCC
Q ss_conf             999999859979999811368876744---66879999999999843-8356765138999998304887
Q gi|254780124|r  115 TADILIFNSTQWIIVDFKYGAGVPVKA---ENNTQLMLYACGALHQY-GDIFGRPEALTLTIIQPRVRTG  180 (388)
Q Consensus       115 tiD~I~~~dg~l~IiDyKtGk~~~v~a---~~n~QL~lYALgA~~~~-~~~~~~~~~v~~~I~qpr~~~~  180 (388)
                      ..|.++...|...|||-||-+.....-   ..-.|--+|++.|+-.- ........++.+....|..+..
T Consensus       244 ktDIvL~~~~~~lIIDTKy~~~~~~~~~~~~~i~s~dLYQm~AYlkn~~~~~~~~~~~~G~LLYp~~~~~  313 (350)
T PRK09736        244 RTDIVLDSKGRRLIIDTKFYSSLTSGRYGTEKLHSNNLYQIYAYLKSQAGGDELADTASGLLLYPKVDED  313 (350)
T ss_pred             CCCEEEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCC
T ss_conf             7627982498189997765344331225778846556799999986031367667745689982688888


No 50 
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=43.65  E-value=13  Score=16.92  Aligned_cols=34  Identities=18%  Similarity=0.327  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHH
Q ss_conf             99999999999997898478523205888786116989
Q gi|254780124|r  273 YVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDIN  310 (388)
Q Consensus       273 w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~  310 (388)
                      |-+.+.+.+.+-+.+|..+    +|+||-..|+|+|.+
T Consensus        60 ~~~~lae~~~~yl~KG~~V----~VeGrL~~r~w~dk~   93 (165)
T PRK06341         60 FNEGLCKVAEQYLKKGAKV----YIEGQLQTRKWTDQS   93 (165)
T ss_pred             HHHHHHHHHHHHHCCCCEE----EEECCEEEEEEECCC
T ss_conf             5289999999973789879----883226873118799


No 51 
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=43.50  E-value=15  Score=16.45  Aligned_cols=11  Identities=18%  Similarity=0.365  Sum_probs=6.2

Q ss_pred             EEEEEEEEEEE
Q ss_conf             89999999985
Q gi|254780124|r  112 ATGTADILIFN  122 (388)
Q Consensus       112 ~~GtiD~I~~~  122 (388)
                      .+|.|--|.++
T Consensus       143 QyGkI~KIvvN  153 (480)
T COG5175         143 QYGKIKKIVVN  153 (480)
T ss_pred             HCCCEEEEEEC
T ss_conf             12543578862


No 52 
>cd06112 citrate_synt_like_1_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, an
Probab=42.20  E-value=23  Score=15.26  Aligned_cols=51  Identities=20%  Similarity=0.334  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             99999999543899999999999999999789847852320588878611698999999986
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      ++++.+.|..+   .+ .+++++|..+.+.+|+.+|||       |.|.|++.|-=+..|++
T Consensus       223 n~~v~~ml~ei---~~-~~~~~~~i~~~l~~~~~i~GF-------GHrvYk~~DPRa~~L~~  273 (373)
T cd06112         223 NEDVLEMLEEI---GS-PENVKAYLDKKLANKQKIWGF-------GHRVYKTKDPRATILQK  273 (373)
T ss_pred             HHHHHHHHHHH---CC-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH
T ss_conf             99999999984---99-888999999987268877888-------87657889942899999


No 53 
>PRK07360 FO synthase subunit 2; Reviewed
Probab=42.15  E-value=18  Score=16.03  Aligned_cols=34  Identities=18%  Similarity=-0.018  Sum_probs=14.8

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHHEECCCCCCE
Q ss_conf             89889999740002426789875300156789826
Q gi|254780124|r  330 KTPKELEQLYKEQKVSDEFWEELQELITRGDGKPV  364 (388)
Q Consensus       330 ~~~~~~ek~~~~~~~~~~~~~~l~~~i~k~~gkp~  364 (388)
                      +++..++..|--.. ++--..++.+-|.+..|.+.
T Consensus       308 ~g~~~~q~aL~~Ga-nD~ggt~~ee~i~~~aG~~~  341 (375)
T PRK07360        308 LGLKLAQEALNCGA-NDLGGTLMEEHITKMAGASG  341 (375)
T ss_pred             CCHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCCCC
T ss_conf             48999999996699-76766566675001226899


No 54 
>KOG1150 consensus
Probab=41.41  E-value=17  Score=16.19  Aligned_cols=14  Identities=43%  Similarity=0.793  Sum_probs=9.3

Q ss_pred             CCCCCCEECCCCCC
Q ss_conf             67898266307886
Q gi|254780124|r  358 RGDGKPVIAPRDIP  371 (388)
Q Consensus       358 k~~gkp~l~p~~d~  371 (388)
                      |..||||.+++|||
T Consensus       139 kKegkpt~ieedDp  152 (250)
T KOG1150         139 KKEGKPTIIEEDDP  152 (250)
T ss_pred             HHCCCCCCCCCCCH
T ss_conf             73389987655688


No 55 
>TIGR00872 gnd_rel 6-phosphogluconate dehydrogenase (decarboxylating); InterPro: IPR004849   This family resembles a larger family of bacterial and eukaryotic 6-phosphogluconate dehydrogenases (Gnd) but differs from it by a deep split in a UPGMA similarity clustering tree and the lack of a central region of about 140 residues. Among complete genomes, it is found is found in Bacillus subtilis and Mycobacterium tuberculosis, both of which also contain Gnd, and in Aquifex aeolicus. .
Probab=41.16  E-value=16  Score=16.35  Aligned_cols=57  Identities=14%  Similarity=0.185  Sum_probs=44.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHH
Q ss_conf             059999999999543899999999999999999789847852320588878611698999
Q gi|254780124|r  253 STNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRA  312 (388)
Q Consensus       253 ~~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~  312 (388)
                      ..-+-+|+|+++.+-+.|.+|+=|+-..|++.--+=.++.|+=---|   -=+||=++++
T Consensus       239 fDfD~~eVArVw~~GSVIrSwL~dLt~~Af~~~~dL~~~~G~v~dSG---EGrWtv~~a~  295 (341)
T TIGR00872       239 FDFDLEEVARVWRRGSVIRSWLLDLTAKAFEESADLEEVEGIVEDSG---EGRWTVKEAV  295 (341)
T ss_pred             CCCCHHHHHHHHCCCCEEEHHHHHHHHHHHHCCCCCCCEEEEECCCC---CCHHHHHHHH
T ss_conf             76874889998708986412688899999750788213223670278---7278999988


No 56 
>KOG2672 consensus
Probab=40.70  E-value=8.6  Score=18.10  Aligned_cols=32  Identities=19%  Similarity=0.209  Sum_probs=16.4

Q ss_pred             CCEEEEEEEEEEEEEC---CEEEEEEEECCCCCCC
Q ss_conf             4405899999999859---9799998113688767
Q gi|254780124|r  108 TEPGATGTADILIFNS---TQWIIVDFKYGAGVPV  139 (388)
Q Consensus       108 ~~~~~~GtiD~I~~~d---g~l~IiDyKtGk~~~v  139 (388)
                      ++-....|+-.....|   -.-+..--||.+.++.
T Consensus       104 G~d~~~ATATIMlmGDTCTRGCRFCsVKTsR~PpP  138 (360)
T KOG2672         104 GGDKSTATATIMLMGDTCTRGCRFCSVKTSRNPPP  138 (360)
T ss_pred             CCCCCCEEEEEEEECCCCCCCCCEEEEECCCCCCC
T ss_conf             89875236898863474346752012103788967


No 57 
>PRK03298 hypothetical protein; Provisional
Probab=40.53  E-value=25  Score=15.09  Aligned_cols=59  Identities=17%  Similarity=0.107  Sum_probs=37.9

Q ss_pred             EEEEEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEC
Q ss_conf             0589999999985-9979999811368876744668799999999998438356765138999998304
Q gi|254780124|r  110 PGATGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRV  177 (388)
Q Consensus       110 ~~~~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~  177 (388)
                      +.-.|.+|.+-++ +|.+.||..|- ++   +.+.-.||.=|--.. +   ..+. ...|+..+.-|..
T Consensus       131 ~T~~G~VDll~~D~~G~~V~VEiKR-ra---~idaV~QL~RYve~l-~---rd~~-~~~VRGIlvAp~I  190 (224)
T PRK03298        131 MTAIGPVDLLCRDADGATVAVEIKR-RG---EIDGVEQLTRYLELL-N---RDPL-LAPVRGVFAAQQI  190 (224)
T ss_pred             CCCCCCEEEEEECCCCCEEEEEEEE-CC---CHHHHHHHHHHHHHH-H---HCCC-CCCEEEEEECCCC
T ss_conf             1798835389987999999999983-06---810899999999998-5---5758-8851499998747


No 58 
>pfam07211 consensus
Probab=40.50  E-value=25  Score=15.09  Aligned_cols=54  Identities=15%  Similarity=0.102  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCC------CCCHHHHHHHHHHCCCCCCHH
Q ss_conf             9999999999999978984785232058887861------169899999998616510000
Q gi|254780124|r  272 SYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRS------FKDINRAQELLTSVLGEEAFK  326 (388)
Q Consensus       272 ~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~------~~d~~~~~~~l~~~~~~~~~~  326 (388)
                      -.-.-|.+|+..+...--.+. ++-.-|+.+.|+      +.|+++..+-|+.+|.++..+
T Consensus        55 ffegli~~Y~~~~~~~DpK~K-~~tpyGkv~srK~k~~~~~~De~~Ll~~lk~n~~~~~Ik  114 (162)
T pfam07211        55 YFEGLVTQYYLKQLTKDPKAK-LSTPYGKVKSRKRKKAPNASDKDQLLNHLKEAGFTEFIK  114 (162)
T ss_pred             HHHHHHHHHHHHHHHCCCCCC-CCCCCCCEEEECCCCCCCCCCHHHHHHHHHHCCCHHHEE
T ss_conf             999999999999873187520-056676411103578856479999999998658333300


No 59 
>COG4950 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.96  E-value=10  Score=17.56  Aligned_cols=62  Identities=15%  Similarity=0.170  Sum_probs=45.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHH---------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             666725764456201346787630---------22005999999999954389999999999999999978
Q gi|254780124|r  226 DSCRFCRAKVRCPALSRHVLLEAT---------KDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNA  287 (388)
Q Consensus       226 ~~CrfC~~k~~Cra~a~~~l~~~~---------~~p~~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~  287 (388)
                      -.|+-|++...|...+.....+-.         -++...+|+.++.|+..+..|..-=+++.-.++.++..
T Consensus        75 ~va~~~~~~~L~~hY~arLap~p~~~~~~~~~~pd~~~es~~RLaai~~yar~L~~~P~~~~r~~l~~L~~  145 (193)
T COG4950          75 TVAQVTGAQRLCAHYAARLAPLPGSESEPSGADPDAARESNERLAAITQYARLLASSPSDIDREALERLYD  145 (193)
T ss_pred             HHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             99986070466678998855588862223567886034550799999999999853965378899998761


No 60 
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=38.90  E-value=26  Score=14.93  Aligned_cols=11  Identities=18%  Similarity=0.531  Sum_probs=6.7

Q ss_pred             EEEEEEEECCC
Q ss_conf             79999811368
Q gi|254780124|r  125 QWIIVDFKYGA  135 (388)
Q Consensus       125 ~l~IiDyKtGk  135 (388)
                      .-..+|+=||-
T Consensus       209 ~~iniDLIyGl  219 (447)
T PRK09058        209 AAVVCDLIFGL  219 (447)
T ss_pred             CCEEEHHHCCC
T ss_conf             63764764279


No 61 
>TIGR01979 sufS cysteine desulfurases, SufS subfamily; InterPro: IPR010970   Cysteine desulphurases are pyridoxal-phosphate enzymes which catalyse the removal of sulphur from L-cysteine to form L-alanine and elemental sulphur. These enzymes have been shown to play an important role in the biosynthesis of iron-sulphur clusters, thionucleosides in tRNA, thiamine, biotin, lipoate and molydopterin    This entry represents a subfamily of NifS-related cysteine desulphurases that are often involved in iron-sulphur cluster formation, which is needed for nitrogen fixation and other vital functions . Many of these enzymes, in addition to cysteine desulphurase activity, also show selenocysteine lyase activity where L-selenocysteine is converted to L-alanine and selenide . Some of these enzymes are much more specific for selenocysteine than cysteine and are thus believed to function in selenium metabolism rather than sulphur metabolism.   Structural studies of the E. coli  and Synechocystis  enzymes indicate that they are homodimers which show a similar fold to other members of the alpha family of pyridoxal-phosphate enzymes .; GO: 0030170 pyridoxal phosphate binding, 0031071 cysteine desulfurase activity, 0006534 cysteine metabolic process.
Probab=37.17  E-value=26  Score=14.99  Aligned_cols=95  Identities=19%  Similarity=0.326  Sum_probs=53.3

Q ss_pred             CHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEC--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             8799999999998438356765138999998304--88775430258988999999999999999985776530477667
Q gi|254780124|r  144 NTQLMLYACGALHQYGDIFGRPEALTLTIIQPRV--RTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHY  221 (388)
Q Consensus       144 n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~--~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~  221 (388)
                      -.+|.-||+   +++..++      .+.||.|+-  +..+.||   +.+++.-.-  ++    ..+++..+-..      
T Consensus       306 E~~L~~yal---~~L~~ip------g~~iyGP~~~~~R~g~is---Fn~~g~HpH--DV----g~~LD~~GiAv------  361 (409)
T TIGR01979       306 EKELTAYAL---ERLGEIP------GLRIYGPRDAEDRGGIIS---FNVEGVHPH--DV----GTILDEEGIAV------  361 (409)
T ss_pred             HHHHHHHHH---HHHHCCC------CEEEECCCCCCCCCCEEE---ECCCCCCCC--HH----HHHCCCCCCEE------
T ss_conf             999999999---9960189------858746877432643333---025888700--22----30122677568------


Q ss_pred             CCCCCCC-----CCCCCCCCCCH-HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             8886666-----72576445620-13467876302200599999999995438999999
Q gi|254780124|r  222 GVNDDSC-----RFCRAKVRCPA-LSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYV  274 (388)
Q Consensus       222 ~~~g~~C-----rfC~~k~~Cra-~a~~~l~~~~~~p~~l~~~e~~~~l~~~~~l~~w~  274 (388)
                       ++|.||     +|=...++||| .+=|           .|.+||-.+...+.-+.+|.
T Consensus       362 -R~GHHCAqPlm~~~~v~atcRASf~~Y-----------NT~ediD~Lv~aL~~v~~~F  408 (409)
T TIGR01979       362 -RSGHHCAQPLMRRFGVPATCRASFYLY-----------NTEEDIDALVEALKKVRKFF  408 (409)
T ss_pred             -EECCHHHHHHHHHCCCCEEEEEEEEEC-----------CCHHHHHHHHHHHHHHHHHH
T ss_conf             -617053248986559963678874103-----------89899999999999999860


No 62 
>KOG0437 consensus
Probab=36.75  E-value=22  Score=15.42  Aligned_cols=59  Identities=20%  Similarity=0.228  Sum_probs=35.0

Q ss_pred             CCCCCCCCC-----CCCCHHHHHHHHHHHCC--------CCCCCHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Q ss_conf             666725764-----45620134678763022--------0059999999999--54389999999999999999
Q gi|254780124|r  226 DSCRFCRAK-----VRCPALSRHVLLEATKD--------PSTNTTVELSKAY--SSISLIKSYVKACEDEMFKR  284 (388)
Q Consensus       226 ~~CrfC~~k-----~~Cra~a~~~l~~~~~~--------p~~l~~~e~~~~l--~~~~~l~~w~~~v~~~a~~~  284 (388)
                      =.||||...     .+||..|++.-.+..+.        |..-.+.++..+-  -...-|..-....+.+++..
T Consensus       841 Lv~r~ietqtlLLaPi~Ph~aeyiw~~~~~~~~~v~~~wP~~s~~~e~~~~~~~yl~~~l~r~~~~l~~~~~~k  914 (1080)
T KOG0437         841 LVFRFIETQTLLLAPICPHLAEYIWRTVLKKNFSVNVGWPFVSPPDEKLGSSALYLKRTLKRLRAELEKQMLKK  914 (1080)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_conf             99999999999874125279999999961688554268997897788754657999999999999988652311


No 63 
>PRK05926 hypothetical protein; Provisional
Probab=36.48  E-value=28  Score=14.68  Aligned_cols=13  Identities=8%  Similarity=0.059  Sum_probs=6.0

Q ss_pred             HHHHHEECCCCCC
Q ss_conf             7530015678982
Q gi|254780124|r  351 ELQELITRGDGKP  363 (388)
Q Consensus       351 ~l~~~i~k~~gkp  363 (388)
                      ++++-|.+..|..
T Consensus       330 ~~eE~I~~aAGa~  342 (371)
T PRK05926        330 HMGEKVFQMASSK  342 (371)
T ss_pred             CCCCEEEHHHCCC
T ss_conf             3133464310279


No 64 
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=36.19  E-value=21  Score=15.61  Aligned_cols=15  Identities=20%  Similarity=0.315  Sum_probs=8.5

Q ss_pred             HHHEECCCCCCEECC
Q ss_conf             300156789826630
Q gi|254780124|r  353 QELITRGDGKPVIAP  367 (388)
Q Consensus       353 ~~~i~k~~gkp~l~p  367 (388)
                      .+|++.-.+.-.|-+
T Consensus       364 ~GLl~~~~~~i~lT~  378 (393)
T PRK08898        364 RGLLERDPTRIRPTP  378 (393)
T ss_pred             CCCEEEECCEEEECH
T ss_conf             898998099999997


No 65 
>PRK12351 methylcitrate synthase; Provisional
Probab=35.30  E-value=30  Score=14.56  Aligned_cols=51  Identities=24%  Similarity=0.360  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             99999999543899999999999999999789847852320588878611698999999986
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      ++++.+.|   ++|.+ .++|++|..+.+.+|+.++||       |.|.|++.|-=+.+|+.
T Consensus       228 n~~v~~ml---~eI~~-~~~v~~~i~~~l~~~~rl~GF-------GHrvYk~~DPRa~~l~~  278 (377)
T PRK12351        228 NEAVMEML---EEIGS-PEEAEAYLRKRLANKEKIMGF-------GHRVYKVSDPRAKILKE  278 (377)
T ss_pred             HHHHHHHH---HHHCC-CHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH
T ss_conf             79999999---99589-257799999998558976577-------87657899936899999


No 66 
>pfam04577 DUF563 Protein of unknown function (DUF563). Family of uncharacterized proteins.
Probab=34.49  E-value=31  Score=14.48  Aligned_cols=31  Identities=16%  Similarity=0.134  Sum_probs=23.8

Q ss_pred             CCCCEECCCCCCCCCCCCHHHHHHHHHHCCCC
Q ss_conf             78523205888786116989999999861651
Q gi|254780124|r  291 IQGYQLVEGRKGNRSFKDINRAQELLTSVLGE  322 (388)
Q Consensus       291 ~~g~Klv~gr~~~r~~~d~~~~~~~l~~~~~~  322 (388)
                      =|-.=|+.=+ +.|++.|+++++.++..+|++
T Consensus       210 rPRL~iisR~-~~R~ilN~~evv~~ae~vGFe  240 (246)
T pfam04577       210 KPRLLIISRR-GSRKILNEDEVVRAAEEVGFE  240 (246)
T ss_pred             CCEEEEEECC-CCCEECCHHHHHHHHHHCCCE
T ss_conf             9869999878-962552899999999984987


No 67 
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=33.91  E-value=31  Score=14.42  Aligned_cols=14  Identities=29%  Similarity=0.449  Sum_probs=5.9

Q ss_pred             HHEECCCCCCEECC
Q ss_conf             00156789826630
Q gi|254780124|r  354 ELITRGDGKPVIAP  367 (388)
Q Consensus       354 ~~i~k~~gkp~l~p  367 (388)
                      +||+...+.-.|-|
T Consensus       412 GLl~~~~~~l~lT~  425 (453)
T PRK13347        412 GLVTIDGGGIRVTP  425 (453)
T ss_pred             CCEEEECCEEEECH
T ss_conf             98899899999997


No 68 
>pfam08011 DUF1703 Protein of unknown function (DUF1703). This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. DUF1703 has the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional beta-strand at the C-terminus.
Probab=33.34  E-value=32  Score=14.36  Aligned_cols=45  Identities=24%  Similarity=0.229  Sum_probs=28.1

Q ss_pred             EEEEEEEEEEE-ECCEEEEEEEECCCCCCCC---C-CCCHHHHHHHHHHH
Q ss_conf             58999999998-5997999981136887674---4-66879999999999
Q gi|254780124|r  111 GATGTADILIF-NSTQWIIVDFKYGAGVPVK---A-ENNTQLMLYACGAL  155 (388)
Q Consensus       111 ~~~GtiD~I~~-~dg~l~IiDyKtGk~~~v~---a-~~n~QL~lYALgA~  155 (388)
                      .+.|++|.++. .++...|+.+|+-+.....   + +.-.|+.-|.....
T Consensus        27 s~~GR~Di~l~p~~~~~~IiE~K~~~~~~~~~~~~~~Al~QI~~k~Y~~~   76 (101)
T pfam08011        27 TNKGRIDLTLKPTYTYIYIFEFKYIKVKDSDKEIAEEALEQIKEYGYAEK   76 (101)
T ss_pred             CCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCHHH
T ss_conf             69994649999748819999999638643101568999999997674088


No 69 
>TIGR01823 PabB-fungal para-aminobenzoate synthase; InterPro: IPR010117   This entry represents the fungal clade of para-aminobenzoate synthase, which acts on chorismate to form para-aminobenzoic acid (PABA), a precursor of folate..
Probab=32.90  E-value=31  Score=14.48  Aligned_cols=73  Identities=15%  Similarity=0.200  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCEECCCCCC
Q ss_conf             8666672576445620134678763022005999999999954389999999999999999978-984785232058887
Q gi|254780124|r  224 NDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNA-GDEIQGYQLVEGRKG  302 (388)
Q Consensus       224 ~g~~CrfC~~k~~Cra~a~~~l~~~~~~p~~l~~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~-G~~~~g~Klv~gr~~  302 (388)
                      -.++|.+=|.|++-+.-.+.+|+.|.  --+.++-|++|.+--+|+|.+=+       ++-+.+ +..||-+==||-- |
T Consensus       632 ~d~~~~~~PiKGTvkk~~~M~lekAr--~iL~~~KemgEnlMI~DLIRnDL-------y~l~~~~~VhVeel~sVeeh-~  701 (851)
T TIGR01823       632 RDDRLKLKPIKGTVKKEEDMSLEKAR--KILKSEKEMGENLMILDLIRNDL-------YELVKKNDVHVEELLSVEEH-A  701 (851)
T ss_pred             CCCCEEECCCCCEECCCCCCCHHHHH--HHHCCCCHHHHHHHHHHHHHHHH-------HHHCCCCCEECCCCCEEHHH-H
T ss_conf             56722322563022107886889999--87268410467878999887538-------98607897422530000112-1


Q ss_pred             CCCCC
Q ss_conf             86116
Q gi|254780124|r  303 NRSFK  307 (388)
Q Consensus       303 ~r~~~  307 (388)
                       |.|.
T Consensus       702 -~VYq  705 (851)
T TIGR01823       702 -RVYQ  705 (851)
T ss_pred             -HHEE
T ss_conf             -2300


No 70 
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=32.66  E-value=21  Score=15.54  Aligned_cols=35  Identities=14%  Similarity=0.319  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHH
Q ss_conf             999999999999997898478523205888786116989
Q gi|254780124|r  272 SYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDIN  310 (388)
Q Consensus       272 ~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~  310 (388)
                      -|-+...+.+..-+.+|..+    +|+||-..|.|+|.+
T Consensus        59 ~~~k~~ae~~~~yl~KG~~V----~VeG~L~~r~y~dkd   93 (152)
T PRK06642         59 IFSEGLVSVVERYVTKGSKL----YIEGSLQTRKWNDNS   93 (152)
T ss_pred             HHHHHHHHHHHHHCCCCCEE----EEEEEEEECCCCCCC
T ss_conf             63389999999865688889----996678753559899


No 71 
>COG0372 GltA Citrate synthase [Energy production and conversion]
Probab=32.21  E-value=33  Score=14.24  Aligned_cols=51  Identities=24%  Similarity=0.376  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHH
Q ss_conf             9999999954389999999999999999978984785232058887861169899999998
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLT  317 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~  317 (388)
                      ++++.+.|..   +.+-.+++++|..+.+.+|+.++||       |.|.|++-|==+++++
T Consensus       235 ne~v~~ml~e---i~~~~~~~~~~v~~~l~~~~~imGF-------GHRVYk~~DPRa~~lk  285 (390)
T COG0372         235 NEAVMKMLEE---IGSSGESAEAYVRKALDRKERIMGF-------GHRVYKNYDPRAKVLK  285 (390)
T ss_pred             HHHHHHHHHH---HCCCCHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHH
T ss_conf             8999999999---6213232999999998569976788-------9776789995599999


No 72 
>cd06106 ScCit3_like Saccharomyces cerevisiae (Sc) 2-methylcitrate synthase Cit3-like. 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxaloacetate (OAA) to form 2-methylcitrate and CoA. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with OAA to form citrate and CoA, the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs.  Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the a
Probab=31.10  E-value=35  Score=14.12  Aligned_cols=56  Identities=20%  Similarity=0.265  Sum_probs=34.7

Q ss_pred             CHHHHHHHH-HHHHHHHHH--HHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             999999999-543899999--999999999999789847852320588878611698999999986
Q gi|254780124|r  256 TTVELSKAY-SSISLIKSY--VKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       256 ~~~e~~~~l-~~~~~l~~w--~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      -++++-+-+ ...+.|.+|  .++|++|+.+.+.+|+.++||       |.|.|+..|-=+..+++
T Consensus       273 ANq~Vl~~l~~m~~~ig~~~~~e~v~~yv~~~l~~g~~i~Gf-------GHrVyk~~DPRa~~lk~  331 (428)
T cd06106         273 AAQEVLRWILEMQKNIGSKATDQDIRDYLWKTLKSGRVVPGY-------GHAVLRKPDPRFTALME  331 (428)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCEEECC-------CEECCCCCCCHHHHHHH
T ss_conf             589999999999998089876899999999854469863202-------60103579947999999


No 73 
>PRK09234 fbiC FO synthase; Reviewed
Probab=30.85  E-value=35  Score=14.09  Aligned_cols=19  Identities=21%  Similarity=0.558  Sum_probs=12.5

Q ss_pred             CCCCCCCCCCCCCCCCCCC
Q ss_conf             7766788866667257644
Q gi|254780124|r  217 SLEHYGVNDDSCRFCRAKV  235 (388)
Q Consensus       217 ~~~~~~~~g~~CrfC~~k~  235 (388)
                      +..+...+.-.|+||.|..
T Consensus       533 NINyTNVC~~~C~FCAF~r  551 (846)
T PRK09234        533 NINFTNICYTGCRFCAFAQ  551 (846)
T ss_pred             CCCHHHHHHCCCCCCCCCC
T ss_conf             7638877551797351447


No 74 
>cd06110 BSuCS-II_like Bacillus subtilis (Bs) citrate synthase (CS)-II_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-II, the major CS of the gram-positive bacterium Bacillus subtilis. A mutation in the gene which encodes BsCS-II (citZ gene) has been described which resulted in a significant loss of CS activity, partial glutamate auxotrophy, and a sporulation deficiency, a
Probab=30.42  E-value=36  Score=14.04  Aligned_cols=51  Identities=22%  Similarity=0.310  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             99999999543899999999999999999789847852320588878611698999999986
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      ++++.+.|..+   .+ .++|++|..+.+.+|+.+|||       |.|.|++.|-=+..|+.
T Consensus       219 n~~v~~ml~~i---~~-~~~v~~~i~~~l~~~~~i~GF-------GHrvY~~~DPRa~~l~~  269 (356)
T cd06110         219 NERVMKMLLEI---GS-VDNVAAYVKDKLANKEKIMGF-------GHRVYKTGDPRAKHLRE  269 (356)
T ss_pred             HHHHHHHHHHH---CC-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH
T ss_conf             99999999984---88-667999999998378988888-------87668888957999999


No 75 
>TIGR01793 cit_synth_euk citrate (Si)-synthase, eukaryotic; InterPro: IPR010109   Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA).    Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH .   This entry includes both mitochondrial and peroxisomal forms of citrate synthase. Peroxisomal forms of the enzyme, recognized by the C-terminal targeting motif SKL, act in the glyoxylate cycle. Eukaryotic homologs include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans (Emericella nidulans).; GO: 0004108 citrate (Si)-synthase activity, 0044262 cellular carbohydrate metabolic process.
Probab=30.10  E-value=35  Score=14.12  Aligned_cols=50  Identities=24%  Similarity=0.339  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHCCCCCCHH
Q ss_conf             9999999999978984785232058887861169899999998616510000
Q gi|254780124|r  275 KACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFK  326 (388)
Q Consensus       275 ~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~~~~~~~~  326 (388)
                      +.+|+|.=..+++|+-||||==--=|..-.+|+-+-  +=+|+..=-|++|+
T Consensus       299 eqlKdy~WktLnsG~VVPGYGHaVLRkTDPRY~cQR--EFALk~LPdDplFk  348 (430)
T TIGR01793       299 EQLKDYVWKTLNSGKVVPGYGHAVLRKTDPRYICQR--EFALKHLPDDPLFK  348 (430)
T ss_pred             HHHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCHH--HHHHHCCCCCHHHH
T ss_conf             678999997605895425766520268898843128--88833178961568


No 76 
>COG1801 Uncharacterized conserved protein [Function unknown]
Probab=29.69  E-value=37  Score=13.96  Aligned_cols=32  Identities=22%  Similarity=0.248  Sum_probs=21.7

Q ss_pred             CCCCCCCCHHHHHC-CCHHHHHHCCCCCCCCHH
Q ss_conf             75618423677871-832388621389998988
Q gi|254780124|r    4 HAFLSASSSHRWLK-CPIAPTLESKIPQTTSIY   35 (388)
Q Consensus         4 HA~LSpSs~~rwl~-CP~s~~Le~~~pd~~S~a   35 (388)
                      +|..|+....||.. -|.-.+.+-+.|..-+-.
T Consensus        47 Ya~p~~~t~~~W~~~~p~~FrFsvK~~~~iTH~   79 (263)
T COG1801          47 YAPPSPETVLRWAEETPDDFRFSVKAPRAITHQ   79 (263)
T ss_pred             CCCCCHHHHHHHHHHCCCCEEEEEEECCCCCCH
T ss_conf             479997999999985899869999855011455


No 77 
>KOG0649 consensus
Probab=28.98  E-value=27  Score=14.81  Aligned_cols=25  Identities=20%  Similarity=0.129  Sum_probs=18.6

Q ss_pred             CCEEEEEEEECCCCCCC-CCCCCHHH
Q ss_conf             99799998113688767-44668799
Q gi|254780124|r  123 STQWIIVDFKYGAGVPV-KAENNTQL  147 (388)
Q Consensus       123 dg~l~IiDyKtGk~~~v-~a~~n~QL  147 (388)
                      ||+.+|.|.||++.+.+ +...|+-+
T Consensus       177 DGtvRvWd~kt~k~v~~ie~yk~~~~  202 (325)
T KOG0649         177 DGTVRVWDTKTQKHVSMIEPYKNPNL  202 (325)
T ss_pred             CCCEEEEECCCCCEEEEECCCCCHHH
T ss_conf             76179876265533677304457211


No 78 
>PRK08207 coproporphyrinogen III oxidase; Provisional
Probab=28.65  E-value=38  Score=13.85  Aligned_cols=17  Identities=29%  Similarity=0.380  Sum_probs=14.2

Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             00599999999995438
Q gi|254780124|r  252 PSTNTTVELSKAYSSIS  268 (388)
Q Consensus       252 p~~l~~~e~~~~l~~~~  268 (388)
                      |..|+.+++..|+..+.
T Consensus       238 PS~Ls~~ql~~ll~~i~  254 (497)
T PRK08207        238 PTSITAEEFEKLLEEIY  254 (497)
T ss_pred             CCCCCHHHHHHHHHHHH
T ss_conf             00299999999999999


No 79 
>TIGR01084 mutY A/G-specific adenine glycosylase; InterPro: IPR005760    The DNA repair enzyme MutY plays an important role in the prevention of DNA mutations resulting from the presence of the oxidatively damaged lesion 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OxoG). 8-OxoG can mispair with 2'-deoxycytidine 5'-triphosphate or with 2'-deoxyadenosine triphosphate during DNA replication, forming C*8-oxoG and A*8-oxoG mispairs. Human MutY is responsible for recognition and removal of the inappropriately inserted adenine in an A=8-oxoG mispair. If unrepaired, the A=8-oxoG mispairs can result in deleterious C:G to A:T transversions.    Multiple forms of mammalian MutY are formed by alternative splicing and locate to the nucleus or mitochondrion, where they have been shown to interact with several other proteins involved in the repair of DNA damage . The HhH-GPD domain within the protein binds the phosphate backbone of the substrate.   This family represents bacterial MutY and a limited number of murine homologs. In rat, the Escherichia coli MutY DNA glycosylase homolog (MYH) is induced in response to mitochondrial DNA damage . ; GO: 0019104 DNA N-glycosylase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=27.72  E-value=35  Score=14.06  Aligned_cols=38  Identities=16%  Similarity=0.250  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             99998577653047766788866667257644562013467876
Q gi|254780124|r  204 GTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLE  247 (388)
Q Consensus       204 a~~~~~~~a~~~~~~~~~~~~g~~CrfC~~k~~Cra~a~~~l~~  247 (388)
                      .+.+++.-|..+.      +....|.-||....|-|..+.+-..
T Consensus       191 nqalmDlGA~iC~------rk~P~C~~CPl~~~C~A~~~~~~~~  228 (297)
T TIGR01084       191 NQALMDLGALICT------RKKPKCDLCPLQDFCLAYKQGTPEE  228 (297)
T ss_pred             HHHHHHCCCCCCC------CCCCCCCCCCHHHHHHHHHCCCHHH
T ss_conf             8899862361037------8478545487066555654277111


No 80 
>pfam09856 DUF2083 Predicted transcriptional regulator (DUF2083). This domain is found in various prokaryotic transcriptional regulatory proteins belonging to the XRE family. Its exact function is, as yet, unknown.
Probab=27.04  E-value=34  Score=14.14  Aligned_cols=24  Identities=25%  Similarity=0.528  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             7888666672576445620134678
Q gi|254780124|r  221 YGVNDDSCRFCRAKVRCPALSRHVL  245 (388)
Q Consensus       221 ~~~~g~~CrfC~~k~~Cra~a~~~l  245 (388)
                      ..+-|-.||-|+ +.-|++||+--+
T Consensus       117 ~~pIG~sCRiC~-R~~C~qRa~Ppi  140 (156)
T pfam09856       117 ATPIGVGCRLCE-RADCPQRAFPPL  140 (156)
T ss_pred             CCCCCCCCCCCC-CCCCCHHCCCCC
T ss_conf             562137411469-889733218988


No 81 
>PRK13627 carnitine operon protein CaiE; Provisional
Probab=26.84  E-value=28  Score=14.73  Aligned_cols=21  Identities=19%  Similarity=0.181  Sum_probs=11.2

Q ss_pred             HHHEECCCCCCEECCCCCCCH
Q ss_conf             300156789826630788620
Q gi|254780124|r  353 QELITRGDGKPVIAPRDIPTN  373 (388)
Q Consensus       353 ~~~i~k~~gkp~l~p~~d~~~  373 (388)
                      .+|-+..++.|.|-..++.+|
T Consensus       174 ~Pl~~~e~~r~~~~~~~~~~p  194 (196)
T PRK13627        174 QPLTQMEENRPRLQGTTDVTP  194 (196)
T ss_pred             CCCCCCCCCCCCCCCCCCCCC
T ss_conf             886446799863357656687


No 82 
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=25.99  E-value=42  Score=13.54  Aligned_cols=37  Identities=27%  Similarity=0.280  Sum_probs=19.4

Q ss_pred             EEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHH
Q ss_conf             9999999985-997999981136887674466879999999
Q gi|254780124|r  113 TGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYAC  152 (388)
Q Consensus       113 ~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYAL  152 (388)
                      .|.+|.+-++ +|...||.+|-++.-+ +|.  .||.=|-.
T Consensus       160 ~G~vDilg~De~G~~viiElKR~ka~~-~Av--~QL~RYv~  197 (253)
T COG1637         160 IGKVDILGRDERGNIVIIELKRRKAGL-SAV--SQLKRYVE  197 (253)
T ss_pred             CCEEEEEEECCCCCEEEEEEECCCCCC-HHH--HHHHHHHH
T ss_conf             425679988689999999994254771-089--99999999


No 83 
>cd06115 AthCS_per_like Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains three Arabidopsis peroxisomal CS proteins, CYS1, -2, and -3 which are involved in the glyoxylate cycle. AthCYS1, in addition to a peroxisomal targeting sequence, has a predicted secretory signal peptide; it may be targeted to both the secretory pathway and the peroxisomes and is thought to be located in the extracellular matrix. AthCSY1 is expr
Probab=25.08  E-value=44  Score=13.43  Aligned_cols=52  Identities=13%  Similarity=0.279  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             999999995438999999999999999997898478523205888786116989999999861
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSV  319 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~  319 (388)
                      ++++.+.|.   .|.+ .++|++|..+.+.+|+.++||       |.|.|+..|-=+..|+..
T Consensus       258 ne~v~~ml~---ei~s-~~~v~~~i~~~l~~~~rimGf-------GHrVYk~~DPRa~ilk~~  309 (410)
T cd06115         258 NEAVLRMLA---EIGT-VENIPAFIEGVKNRKRKLSGF-------GHRVYKNYDPRAKIIKKL  309 (410)
T ss_pred             HHHHHHHHH---HHCC-HHHHHHHHHHHHCCCCCCCCC-------CCCCCCCCCCHHHHHHHH
T ss_conf             899999999---9647-223799999987167876778-------987688888277999999


No 84 
>PRK08173 DNA topoisomerase III; Validated
Probab=24.45  E-value=45  Score=13.36  Aligned_cols=32  Identities=13%  Similarity=0.205  Sum_probs=23.6

Q ss_pred             HCCCCHHHHHHHHHHCCCCHHHHHHHHHHEECCCCCC
Q ss_conf             0138988999974000242678987530015678982
Q gi|254780124|r  327 RILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKP  363 (388)
Q Consensus       327 ~~l~~~~~~ek~~~~~~~~~~~~~~l~~~i~k~~gkp  363 (388)
                      .+.||+.||.||+.+.+     -++|.+|+-+..|+|
T Consensus       766 ~k~i~~~~~~kLl~~gk-----T~li~gF~S~k~gr~  797 (857)
T PRK08173        766 QQEISREQMAKLLTDGK-----TDLLPGFKSSRTGRN  797 (857)
T ss_pred             CCCCCHHHHHHHHHCCC-----CCHHCCCEECCCCCC
T ss_conf             98789999999997599-----103203343778996


No 85 
>cd06118 citrate_synt_like_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and 
Probab=24.43  E-value=45  Score=13.36  Aligned_cols=46  Identities=22%  Similarity=0.419  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             543899999999999999999789847852320588878611698999999986
Q gi|254780124|r  265 SSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       265 ~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      ...+.+.+ .++++++..+.+.+|+.++||       |.|.|++.|-=+.+|+.
T Consensus       224 ~~l~~i~~-~~~~~~~i~~~l~~~~~i~GF-------GHrvYk~~DPRa~~l~~  269 (358)
T cd06118         224 KMLLEIGT-PENVEAYIWKKLANKRRIMGF-------GHRVYKTYDPRAKILKE  269 (358)
T ss_pred             HHHHHHCC-HHHHHHHHHHHHCCCCCCCCC-------CCCCCCCCCCHHHHHHH
T ss_conf             99999688-565899999974046777787-------87657889955899999


No 86 
>pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown.
Probab=24.40  E-value=45  Score=13.35  Aligned_cols=59  Identities=19%  Similarity=0.241  Sum_probs=37.4

Q ss_pred             EEEEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEC
Q ss_conf             589999999985-9979999811368876744668799999999998438356765138999998304
Q gi|254780124|r  111 GATGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRV  177 (388)
Q Consensus       111 ~~~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~  177 (388)
                      .-.|.+|.+-++ +|.+.||..|--++   +.+.-.||.=|--...+.    +. ...|+..+.-|..
T Consensus       133 T~~G~VDil~~D~~G~~VvVEvKRr~a---~idaV~QL~RYve~l~rd----~~-~~~VRGIlvAp~I  192 (228)
T pfam01939       133 IAHGIVDILGKDEDGNIVILELKRRKA---DLHAVSQLKRYVDSLKED----YV-EAKVRGVLVAPSI  192 (228)
T ss_pred             CCCCCEEEEEECCCCCEEEEEEEEECC---CHHHHHHHHHHHHHHHHC----CC-CCCCEEEEECCCC
T ss_conf             588736689987999999999974037---820799999999998655----48-8860399999858


No 87 
>KOG2457 consensus
Probab=23.50  E-value=27  Score=14.87  Aligned_cols=23  Identities=22%  Similarity=0.496  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCCCCCCCCHHH--HHH
Q ss_conf             88866667257644562013--467
Q gi|254780124|r  222 GVNDDSCRFCRAKVRCPALS--RHV  244 (388)
Q Consensus       222 ~~~g~~CrfC~~k~~Cra~a--~~~  244 (388)
                      +|....|.-||..++|||+.  |.|
T Consensus       290 Tpq~P~CS~CPvss~CrA~q~~Eqn  314 (555)
T KOG2457         290 TPQKPSCSSCPVSSQCRAFQLSEQN  314 (555)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf             5799876778728899887676423


No 88 
>TIGR01311 glycerol_kin glycerol kinase; InterPro: IPR005999    Glycerol kinase (2.7.1.30 from EC) is a bacterial sugar kinase which catalyzes the Mg-ATP-dependent phosphorylation of glycerol to yield glycerol 3-phosphate. The enzyme from Escherichia coli is an allosteric regulatory enzyme whose activity is inhibited by fructose 1,6-bisphosphate (FBP) and the glucose-specific phosphocarrier of the phosphoenolpyruvate:glycose phosphotransferase system, IIA(Glc), structural studies suggest a nucleophilic in-line transfer mechanism for the ATP-dependent phosphorylation of glycerol by glycerol kinase .; GO: 0004370 glycerol kinase activity, 0006072 glycerol-3-phosphate metabolic process.
Probab=23.35  E-value=19  Score=15.90  Aligned_cols=37  Identities=19%  Similarity=0.123  Sum_probs=22.7

Q ss_pred             EEEEEEEEEEEE---ECC---EEEEEEEECCCCC-----CCCCCCCHHH
Q ss_conf             058999999998---599---7999981136887-----6744668799
Q gi|254780124|r  110 PGATGTADILIF---NST---QWIIVDFKYGAGV-----PVKAENNTQL  147 (388)
Q Consensus       110 ~~~~GtiD~I~~---~dg---~l~IiDyKtGk~~-----~v~a~~n~QL  147 (388)
                      --+|||||.-++   .+|   ..||.|+ |.-+.     ...-+.+.+|
T Consensus       163 ~LlFGTiDTWL~WnLTGG~nG~~HvTDv-tNASRT~LfNl~tl~WD~eL  210 (518)
T TIGR01311       163 ELLFGTIDTWLIWNLTGGVNGKVHVTDV-TNASRTMLFNLHTLEWDDEL  210 (518)
T ss_pred             CCEECCCHHHHHHHHCCCCCCCEEECCC-CCHHHHHHCCCHHHHHHHHH
T ss_conf             8433250246675315897886553378-61468764140121000899


No 89 
>TIGR00770 Dcu transporter, anaerobic C4-dicarboxylate uptake (Dcu) family; InterPro: IPR004668   These proteins are members of the C4-Dicarboxylate Uptake (Dcu) family. Most proteins in this family are predicted to have 12 GES predicted transmembrane regions; however the one member whose membrane topology has been experimentally determined has 10 transmembrane regions, with both the N- and C-termini localized to the periplasm . The DcuA and DcuB proteins are involved in the transport of aspartate, malate, fumarate and succinate in many species , , , and are thought to function as antiporters with any two of these substrates. Since DcuA is encoded in an operon with the gene for aspartase, and DcuB is encoded in an operon with the gene for fumarase, their physiological functions may be to catalyze aspartate:fumarate and fumarate:malate exchange during the anaerobic utilization of aspartate and fumarate, respectively . The Escherichia coli DcuA and DcuB proteins have very different expression patterns . DcuA is constitutively expressed; DcuB is strongly induced anaerobically by FNR and C4-dicarboxylates, while it is repressed by nitrate and subject to CRP-mediated catabolite repression.; GO: 0015556 C4-dicarboxylate transmembrane transporter activity, 0015740 C4-dicarboxylate transport, 0016021 integral to membrane.
Probab=23.15  E-value=29  Score=14.64  Aligned_cols=11  Identities=9%  Similarity=0.175  Sum_probs=5.5

Q ss_pred             HHHHHHHCCCC
Q ss_conf             99999724576
Q gi|254780124|r   45 LLAHCLEQGVD   55 (388)
Q Consensus        45 llE~~l~~~l~   55 (388)
                      ++|.+||+.-+
T Consensus        72 iAEKlLRrnPK   82 (447)
T TIGR00770        72 IAEKLLRRNPK   82 (447)
T ss_pred             HHHHHHCCCCC
T ss_conf             99897416997


No 90 
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=22.88  E-value=48  Score=13.16  Aligned_cols=73  Identities=21%  Similarity=0.206  Sum_probs=41.0

Q ss_pred             HHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECC-EEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC
Q ss_conf             9998503787368877553200044058999999998599-799998113688767446687999999999984383567
Q gi|254780124|r   85 LAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNST-QWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFG  163 (388)
Q Consensus        85 ~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg-~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~  163 (388)
                      +.+..+..++.----||+=+...    .-|++|...+.|| ....+.-|.+.  ...+.+.-|+.-||.-.-..++...+
T Consensus        32 lp~L~slGwdi~nPkEV~PEe~t----~~GraDyalikd~kvfafieak~ls--~~~akd~qq~~~Yav~~Gv~~~iVtn  105 (284)
T COG2810          32 LPFLSSLGWDIDNPKEVRPEEKT----EEGRADYALIKDGKVFAFIEAKNLS--VNPAKDVQQLAKYAVDKGVEVGIVTN  105 (284)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCC----CCCCCCEEEEECCCEEEEEECCCCC--CCCHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             99999707778990205864245----5576544888569389987211347--57268999999998852837999967


No 91 
>KOG3300 consensus
Probab=22.40  E-value=50  Score=13.10  Aligned_cols=33  Identities=6%  Similarity=0.183  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCC
Q ss_conf             389999999999999999978984785232058
Q gi|254780124|r  267 ISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEG  299 (388)
Q Consensus       267 ~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~g  299 (388)
                      +..=..|++.++.+...++.-=+.|||||+=|-
T Consensus        80 AErDr~~l~~lrkn~eeEaeiMKdVPgWkvGEp  112 (146)
T KOG3300          80 AERDRRFLSELRKNLEEEAEIMKDVPGWKVGEP  112 (146)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             887799999999868889999704998623765


No 92 
>cd06111 DsCS_like Cold-active citrate synthase (CS) from an Antarctic bacterial strain DS2-3R (Ds)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. DsCS, compared with CS from the hyperthermophile Pyrococcus furiosus (not included in this group), has an increase in the size of surface loops, a higher proline content in the loop regions, a more accessible active site, and a highe
Probab=22.18  E-value=50  Score=13.07  Aligned_cols=50  Identities=14%  Similarity=0.251  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHH
Q ss_conf             9999999954389999999999999999978984785232058887861169899999998
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLT  317 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~  317 (388)
                      ++.+.+.|   +++.+ .+++++|..+.+.+|+.++||       |.|.|++.|-=+..|+
T Consensus       219 n~~v~~ml---~ei~~-~~~~~~~i~~~l~~~~~i~GF-------GHrvYk~~DPRa~~l~  268 (362)
T cd06111         219 NEAVMHMM---LEIDD-PEKAAQWMLDALARKEKVMGF-------GHRVYKSGDSRVPTME  268 (362)
T ss_pred             HHHHHHHH---HHHCC-HHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCCHHHHH
T ss_conf             89999999---98378-122699999998468877888-------8755778895059999


No 93 
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein; InterPro: IPR011903   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    This entry of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different..
Probab=21.98  E-value=32  Score=14.32  Aligned_cols=21  Identities=29%  Similarity=0.583  Sum_probs=11.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             6666725764456201346787630
Q gi|254780124|r  225 DDSCRFCRAKVRCPALSRHVLLEAT  249 (388)
Q Consensus       225 g~~CrfC~~k~~Cra~a~~~l~~~~  249 (388)
                      ...|-|||...    +.-|+++++.
T Consensus       156 TPtCPYCP~AV----~mAH~fA~~~  176 (237)
T TIGR02187       156 TPTCPYCPRAV----LMAHKFALAN  176 (237)
T ss_pred             ECCCCCHHHHH----HHHHHHHHHC
T ss_conf             56899725799----9999999835


No 94 
>COG3894 Uncharacterized metal-binding protein [General function prediction only]
Probab=21.89  E-value=27  Score=14.84  Aligned_cols=24  Identities=33%  Similarity=0.331  Sum_probs=19.0

Q ss_pred             EEEEEEEECCCCCCCCCCCCHHHH
Q ss_conf             799998113688767446687999
Q gi|254780124|r  125 QWIIVDFKYGAGVPVKAENNTQLM  148 (388)
Q Consensus       125 ~l~IiDyKtGk~~~v~a~~n~QL~  148 (388)
                      ..++||+|+|+-+.+.-..|+|++
T Consensus       177 ~aqlVDL~sgevv~t~~T~n~ql~  200 (614)
T COG3894         177 RAQLVDLKSGEVVATVITSNPQLP  200 (614)
T ss_pred             EEEEEECCCCCEEEEEECCCCCCC
T ss_conf             257875167867886522589877


No 95 
>PRK04247 hypothetical protein; Provisional
Probab=21.56  E-value=51  Score=12.99  Aligned_cols=56  Identities=16%  Similarity=0.204  Sum_probs=29.8

Q ss_pred             EEEEEEEEEEE-CCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEE
Q ss_conf             89999999985-997999981136887674466879999999999843835676513899999830
Q gi|254780124|r  112 ATGTADILIFN-STQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPR  176 (388)
Q Consensus       112 ~~GtiD~I~~~-dg~l~IiDyKtGk~~~v~a~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr  176 (388)
                      -.|.+|.+-++ +|.+.||..|-.++-   .+.-.||.=|--......      ...|+..+.-|.
T Consensus       158 ~~G~VDil~~D~~G~~V~VEvKR~ra~---idaV~QL~RYve~l~~~~------~~~VRGIlvAp~  214 (250)
T PRK04247        158 PAGIIDILGRDKEGNLVVLELKRRRAG---LSAVSQLKRYVEAYREEL------GAKVRGILVAPS  214 (250)
T ss_pred             CCCCEEEEEECCCCCEEEEEEEECCCC---CCHHHHHHHHHHHHHHHC------CCCCEEEEECCC
T ss_conf             988464899879989999999713378---147999999999987636------998219999885


No 96 
>cd06100 CCL_ACL-C Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CC
Probab=21.51  E-value=52  Score=12.99  Aligned_cols=56  Identities=13%  Similarity=0.111  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             999999995438-999999999999999997898478523205888786116989999999861
Q gi|254780124|r  257 TVELSKAYSSIS-LIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSV  319 (388)
Q Consensus       257 ~~e~~~~l~~~~-~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~  319 (388)
                      ++...+.+..+. .-.....++..++.+....|+.+|||    |   .|.|++.|--...|++.
T Consensus        84 ~e~~~~ml~~~~~~~~~~~~~~~~~v~~~~~~~~~ipGf----G---H~vyk~~DPRa~~L~~~  140 (227)
T cd06100          84 GEGAARLFKEAVDSGDALDAAAAEFVAEYRAAKKRIPGF----G---HPVHKNPDPRVPRLLEL  140 (227)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCC----C---CCCCCCCCCHHHHHHHH
T ss_conf             699999999998647762889999999998659977788----9---88799999459999999


No 97 
>cd06103 ScCS-like Saccharomyces cerevisiae (Sc) citrate synthase (CS)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs.  Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homo
Probab=21.24  E-value=52  Score=12.95  Aligned_cols=55  Identities=16%  Similarity=0.247  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHH-HHHHH--HHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             99999999543-89999--9999999999999789847852320588878611698999999986
Q gi|254780124|r  257 TVELSKAYSSI-SLIKS--YVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTS  318 (388)
Q Consensus       257 ~~e~~~~l~~~-~~l~~--w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~  318 (388)
                      ++++-+.|..+ +.+-.  -.+.|++|+.+.+.+|+.++||       |.|.|+..|-=+..+++
T Consensus       274 Ne~Vl~ml~~i~~~~g~~~s~e~v~~~v~~~l~~~~~imGf-------GHrVYk~~DPRa~ilk~  331 (426)
T cd06103         274 NQEVLKWLLKMQKELGKDVSDEELEKYIWDTLNSGRVVPGY-------GHAVLRKTDPRFTCQRE  331 (426)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHH
T ss_conf             89999999999987288888899999999987169943267-------87657789946999999


No 98 
>PRK12350 citrate synthase 2; Provisional
Probab=21.12  E-value=53  Score=12.93  Aligned_cols=52  Identities=13%  Similarity=0.302  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             999999995438999999999999999997898478523205888786116989999999861
Q gi|254780124|r  257 TVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSV  319 (388)
Q Consensus       257 ~~e~~~~l~~~~~l~~w~~~v~~~a~~~~~~G~~~~g~Klv~gr~~~r~~~d~~~~~~~l~~~  319 (388)
                      ++.+.+.|..+   .+ .++++++..+.+..|+.++||       |.|.|++.|-=+.+|+..
T Consensus       206 ne~v~~ml~~i---~~-~~~~~~~i~~~l~~~~rimGF-------GHrVYk~~DPRa~~lk~~  257 (352)
T PRK12350        206 PGRVLPMLDAI---ER-TGDARGWVKGALDRGERLMGF-------GHRVYRAEDPRARVLRAA  257 (352)
T ss_pred             HHHHHHHHHHH---CC-CCCHHHHHHHHHHCCCCCCCC-------CCCCCCCCCCHHHHHHHH
T ss_conf             99999999984---67-002899999998536765567-------887788899358999999


No 99 
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=20.45  E-value=54  Score=12.84  Aligned_cols=19  Identities=11%  Similarity=0.401  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             3899999999999999999
Q gi|254780124|r  267 ISLIKSYVKACEDEMFKRL  285 (388)
Q Consensus       267 ~~~l~~w~~~v~~~a~~~~  285 (388)
                      +++|....+.|-+.+++++
T Consensus        47 IPElReRik~vAe~~~~~v   65 (185)
T PRK04424         47 IPELRERIKHVAEKNYDKV   65 (185)
T ss_pred             CHHHHHHHHHHHHHHHHHH
T ss_conf             8789999999999747640


No 100
>pfam05813 Orthopox_F7 Orthopoxvirus F7 protein.
Probab=20.01  E-value=33  Score=14.24  Aligned_cols=14  Identities=43%  Similarity=0.914  Sum_probs=7.2

Q ss_pred             CCC-CCCCCCCCCCH
Q ss_conf             666-72576445620
Q gi|254780124|r  226 DSC-RFCRAKVRCPA  239 (388)
Q Consensus       226 ~~C-rfC~~k~~Cra  239 (388)
                      +.| |||++|.--.-
T Consensus         7 sccgrfcdaknknk~   21 (82)
T pfam05813         7 SCCGRFCDAKNKNKN   21 (82)
T ss_pred             CHHHHHCCCCCCCCC
T ss_conf             222102033333532


Done!