Query         gi|254780881|ref|YP_003065294.1| Mrp protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 101
No_of_seqs    106 out of 1506
Neff          7.9 
Searched_HMMs 39220
Date          Mon May 30 01:21:16 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780881.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11670 putative ATPase; Prov  99.8 1.6E-20 4.1E-25  136.5  10.0   99    3-101    11-113 (369)
  2 TIGR02945 SUF_assoc FeS assemb  99.7 2.4E-17 6.2E-22  118.5   4.9   89    7-95      1-90  (96)
  3 TIGR03406 FeS_long_SufT probab  99.7 1.2E-16 3.1E-21  114.6   6.7   91    3-93     72-167 (174)
  4 pfam01883 DUF59 Domain of unkn  99.7 2.3E-16   6E-21  113.0   7.5   75    5-79      1-76  (76)
  5 COG2151 PaaD Predicted metal-s  99.6 9.6E-16 2.4E-20  109.6   6.1   94    2-95     10-105 (111)
  6 TIGR02159 PA_CoA_Oxy4 phenylac  98.9 6.1E-09 1.6E-13   71.3   6.7   73   16-88      1-75  (152)
  7 TIGR03341 YhgI_GntY IscR-regul  89.9    0.94 2.4E-05   25.2   5.5   76    5-84    106-184 (190)
  8 PRK11190 putative DNA uptake p  83.2     3.1   8E-05   22.2   5.2   76    5-84    107-186 (192)
  9 pfam01106 NifU NifU-like domai  82.3     2.2 5.7E-05   23.1   4.1   62   10-75      2-65  (68)
 10 TIGR01748 rhaA L-rhamnose isom  82.1     2.1 5.4E-05   23.2   3.9   71    8-78     18-91  (415)
 11 pfam09650 PHA_gran_rgn Putativ  79.7       3 7.7E-05   22.3   4.0   45   25-69     42-86  (87)
 12 TIGR02830 spore_III_AG stage I  79.7     3.2 8.3E-05   22.2   4.2   34   52-85     62-95  (193)
 13 COG5133 Uncharacterized conser  78.8       6 0.00015   20.7   5.6   77    4-80     54-140 (181)
 14 KOG3381 consensus               74.0       6 0.00015   20.6   4.3   77    5-81     35-121 (161)
 15 TIGR01608 citD citrate lyase a  71.0     8.2 0.00021   19.9   4.4   46   34-80     19-66  (95)
 16 cd00371 HMA Heavy-metal-associ  60.0     6.5 0.00017   20.4   2.1   26   58-83     12-37  (63)
 17 TIGR02668 moaA_archaeal probab  57.4      18 0.00045   18.0   4.9   78    4-83     74-167 (324)
 18 pfam00403 HMA Heavy-metal-asso  56.7     8.7 0.00022   19.7   2.3   26   57-82     11-36  (62)
 19 TIGR01162 purE phosphoribosyla  48.5      25 0.00064   17.2   3.9   44   57-101    12-62  (159)
 20 pfam03780 DUF322 Protein of un  47.6      26 0.00066   17.1   4.7   43   38-80     57-103 (108)
 21 TIGR02052 MerP mercuric transp  46.7       9 0.00023   19.7   1.1   32   42-79     24-58  (92)
 22 TIGR03123 one_C_unchar_1 proba  41.9      12  0.0003   19.0   1.1   47   38-84     18-64  (318)
 23 pfam08921 DUF1904 Domain of un  41.8      32 0.00081   16.6   5.7   73    8-82     19-96  (107)
 24 pfam04953 consensus             40.9      33 0.00084   16.5   4.1   38   42-80     28-66  (97)
 25 cd00756 MoaE MoaE family. Memb  40.1      34 0.00087   16.4   4.8   67    9-78      3-69  (124)
 26 TIGR02610 PHA_gran_rgn putativ  38.1      27 0.00069   17.0   2.4   47   22-68     42-88  (91)
 27 COG4806 RhaA L-rhamnose isomer  37.3      38 0.00096   16.2   4.5   71    8-78     22-95  (419)
 28 PRK11033 zntA zinc/cadmium/mer  37.2      25 0.00064   17.2   2.1   42   39-83     47-88  (739)
 29 COG3965 Predicted Co/Zn/Cd cat  36.4      39   0.001   16.1   5.2   39   48-86    275-313 (314)
 30 PRK13253 citrate lyase subunit  34.4      42  0.0011   15.9   5.3   41   38-80     26-66  (92)
 31 TIGR00884 guaA_Cterm GMP synth  33.3      18 0.00046   17.9   0.9   30   55-84    284-313 (319)
 32 TIGR02544 III_secr_YscJ type I  32.3      46  0.0012   15.7   4.5   67    9-84     75-142 (203)
 33 PRK10671 copA copper exporting  29.9      50  0.0013   15.4   4.8   40   41-83     99-138 (834)
 34 PRK10503 multidrug efflux syst  29.6      51  0.0013   15.4   6.7   18   60-77    169-186 (1040)
 35 PRK05783 hypothetical protein;  27.1      57  0.0014   15.2   4.5   65   14-79     13-81  (84)
 36 COG0041 PurE Phosphoribosylcar  27.0      57  0.0015   15.2   3.8   43   58-101    17-65  (162)
 37 pfam01251 Ribosomal_S7e Riboso  26.6      58  0.0015   15.1   4.8   73    5-77     14-91  (189)
 38 pfam01514 YscJ_FliF Secretory   25.7      60  0.0015   15.0   4.3   33   52-84    109-141 (206)
 39 PRK00435 ef1B elongation facto  25.6      60  0.0015   15.0   2.5   68    3-80     16-85  (88)
 40 TIGR00003 TIGR00003 copper ion  25.6      43  0.0011   15.8   1.8   27   57-83     13-39  (66)
 41 TIGR01923 menE O-succinylbenzo  24.8      63  0.0016   14.9   2.5   32   58-89    403-434 (490)
 42 PRK06156 hypothetical protein;  24.6      63  0.0016   14.9   4.9   59   18-79    369-427 (522)
 43 cd04887 ACT_MalLac-Enz ACT_Mal  24.6      63  0.0016   14.9   4.2   51   20-77     22-72  (74)
 44 pfam02391 MoaE MoaE protein. T  24.6      63  0.0016   14.9   4.7   68    8-78     10-77  (117)
 45 TIGR02347 chap_CCT_zeta T-comp  23.6      66  0.0017   14.8   2.6   57   13-70    342-409 (548)
 46 pfam09580 Spore_YhcN_YlaJ Spor  23.5      67  0.0017   14.8   5.1   42   36-77     88-130 (169)
 47 pfam00873 ACR_tran AcrB/AcrD/A  22.8      69  0.0018   14.7   5.6   35   42-76    672-706 (1021)
 48 KOG4656 consensus               22.4      70  0.0018   14.6   3.0   25   56-80     18-42  (247)
 49 PRK10614 multidrug efflux syst  21.4      74  0.0019   14.5   6.6   19   59-77    159-177 (1025)
 50 TIGR01054 rgy reverse gyrase;   21.1      53  0.0013   15.3   1.5   42    2-45    840-884 (1843)
 51 PRK13614 lipoprotein LpqB; Pro  21.0      75  0.0019   14.5   4.9   48   32-79    238-288 (573)
 52 COG2608 CopZ Copper chaperone   20.5      77   0.002   14.4   4.4   36   43-81      4-39  (71)
 53 TIGR00855 L12 ribosomal protei  20.0      66  0.0017   14.8   1.8   18    1-18      1-18  (131)

No 1  
>PRK11670 putative ATPase; Provisional
Probab=99.84  E-value=1.6e-20  Score=136.47  Aligned_cols=99  Identities=18%  Similarity=0.292  Sum_probs=90.9

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEC
Q ss_conf             03589999998414187999762323870101336987999999672222068999999999985398534069999707
Q gi|254780881|r    3 QILKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTEN   82 (101)
Q Consensus         3 ~~~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~   82 (101)
                      +-++++|+++|++|.||++++||+|+|||+++.++++++.|.|.++++.|+.+++++++++++|++++|++++++.++++
T Consensus        11 ~~l~~~v~~~L~~v~dP~~~~~iv~lg~v~~i~i~~~~v~i~l~l~~~~~~~~~~~~~~~~~~l~~~~~~~~v~~~~~~~   90 (369)
T PRK11670         11 EALRAMVAGTLANFQHPTLKHNLTTLKALHHVAWMDDTLHIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHN   90 (369)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCEECCCCEEEEEEECCEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEC
T ss_conf             89999999998077798999880037970169997999999999688898879999999999998578974589999740


Q ss_pred             CCC----CCCCCCCCCCEEEEEC
Q ss_conf             898----7321569985588859
Q gi|254780881|r   83 KNP----PQQRNNLNVKKFVAVA  101 (101)
Q Consensus        83 ~~~----~~~~~~~gvKnIIAVA  101 (101)
                      ...    +....++|||||||||
T Consensus        91 ~~~~~~~~~~~~~~~v~~vIAVa  113 (369)
T PRK11670         91 IATLKRVNNQPGVNGVKNIIAVS  113 (369)
T ss_pred             CCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             45645556678888868899998


No 2  
>TIGR02945 SUF_assoc FeS assembly SUF system protein; InterPro: IPR014291   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry is a subset of the larger DUF59 family. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here are all found as part of the FeS assembly SUF system locus, in a subset of SUF-positive proteobacteria. .
Probab=99.69  E-value=2.4e-17  Score=118.54  Aligned_cols=89  Identities=17%  Similarity=0.194  Sum_probs=83.4

Q ss_pred             HHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCC-CEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCC
Q ss_conf             99999984141879997623238701013369-87999999672222068999999999985398534069999707898
Q gi|254780881|r    7 NQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVH-NTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKNP   85 (101)
Q Consensus         7 ~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~-~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~~   85 (101)
                      ++|.++|++|.|||..-||++||+||.|+++| ++|+|.++|++|+||.+..+=..+++|+.+++||++|+|+||++++|
T Consensus         1 ~~~i~alktVYDPEIPvnIYeLGLIY~i~i~Dd~~V~I~MTLTaPgCPvAgemP~~V~~aV~~v~GV~~v~VelvwdPPW   80 (96)
T TIGR02945         1 EEVIEALKTVYDPEIPVNIYELGLIYKIEISDDRHVHIDMTLTAPGCPVAGEMPGWVEDAVGQVPGVSSVEVELVWDPPW   80 (96)
T ss_pred             CHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCCCCCCCCHHHHHHHHCCCCCCCEEEEEEEECCCC
T ss_conf             92455420268998876610358675887658986788775178568422452268899733388985025776767866


Q ss_pred             CCCCCCCCCC
Q ss_conf             7321569985
Q gi|254780881|r   86 PQQRNNLNVK   95 (101)
Q Consensus        86 ~~~~~~~gvK   95 (101)
                      ...+.....|
T Consensus        81 ~~~RMSdeAr   90 (96)
T TIGR02945        81 DMDRMSDEAR   90 (96)
T ss_pred             CCCCCCHHHH
T ss_conf             9233677899


No 3  
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=99.67  E-value=1.2e-16  Score=114.63  Aligned_cols=91  Identities=14%  Similarity=0.115  Sum_probs=84.1

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCC-----CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf             03589999998414187999762323870101336-----9879999996722220689999999999853985340699
Q gi|254780881|r    3 QILKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIV-----HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVV   77 (101)
Q Consensus         3 ~~~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~-----~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V   77 (101)
                      +..+++|+++|++|.|||.+-|||++|+|+++.++     +++|.|.+++++|+|++...|..++++++..++|+++|+|
T Consensus        72 ~~~E~~vweaLk~V~DPEIpVnIVdLGLIY~v~i~~~~~~~~~V~I~MTLTapgCpmg~~i~~dv~~~v~~v~~v~~v~V  151 (174)
T TIGR03406        72 EDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEGQFRVDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEV  151 (174)
T ss_pred             CHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEECCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             42099999998415598887544863025799987647889779999960479998317999999999977999664999


Q ss_pred             EEEECCCCCCCCCCCC
Q ss_conf             9970789873215699
Q gi|254780881|r   78 TLTENKNPPQQRNNLN   93 (101)
Q Consensus        78 ~lt~~~~~~~~~~~~g   93 (101)
                      .++++++|.+......
T Consensus       152 elV~dPpW~~dmmSee  167 (174)
T TIGR03406       152 ELVFDPPWSREMMSEA  167 (174)
T ss_pred             EEEECCCCCHHHCCHH
T ss_conf             9998899893347799


No 4  
>pfam01883 DUF59 Domain of unknown function DUF59. This family includes prokaryotic proteins of unknown function. The family also includes PhaH from Pseudomonas putida. PhaH forms a complex with PhaF, PhaG, and PhaI, which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid. So members of this family may all be components of ring hydroxylating complexes.
Probab=99.66  E-value=2.3e-16  Score=113.01  Aligned_cols=75  Identities=21%  Similarity=0.303  Sum_probs=71.8

Q ss_pred             CHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCC-CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             589999998414187999762323870101336-987999999672222068999999999985398534069999
Q gi|254780881|r    5 LKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIV-HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL   79 (101)
Q Consensus         5 ~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~-~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l   79 (101)
                      ++++|+++|++|.||+++.||+++|+|+++.++ +|++.|.+++++++||..+.|.+++++++.+++|+++|+|.+
T Consensus         1 l~e~I~~aL~~V~DPEl~~~Iv~LGlI~~i~v~~~g~v~I~~~lT~~~CP~~~~i~~~i~~~l~~v~gv~~V~V~l   76 (76)
T pfam01883         1 LKEAILEALKTVIDPELPVDIVDLGLVYEVDIDDDGNVKVKMTLTTPGCPLADLIALDVREALLELPGVEDVEVEL   76 (76)
T ss_pred             CHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEC
T ss_conf             9789999982778999997800245368999857984999999589999837899999999998399940789979


No 5  
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=99.61  E-value=9.6e-16  Score=109.56  Aligned_cols=94  Identities=18%  Similarity=0.223  Sum_probs=86.0

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCC--CEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             6035899999984141879997623238701013369--87999999672222068999999999985398534069999
Q gi|254780881|r    2 NQILKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVH--NTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL   79 (101)
Q Consensus         2 s~~~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~--~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l   79 (101)
                      ...++++|+++|++|.||+.+.||+++|+|+++.+++  +.+.|.+++++++|+..+.+..++++++..++|+++++|.+
T Consensus        10 ~~~~~~~i~~aL~~V~DPEi~idIvdLGLVy~v~i~~~~~~v~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l   89 (111)
T COG2151          10 IKVTLEDILEALKTVIDPEIGIDIVDLGLVYEVDIDDVDGLVKVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL   89 (111)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEEEECCEEEEEEECCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf             36669999998534779666603576310799997267746999995178888820788999999998468813079999


Q ss_pred             EECCCCCCCCCCCCCC
Q ss_conf             7078987321569985
Q gi|254780881|r   80 TENKNPPQQRNNLNVK   95 (101)
Q Consensus        80 t~~~~~~~~~~~~gvK   95 (101)
                      +++++|...+..+..|
T Consensus        90 ~~~p~Wt~~~ms~ear  105 (111)
T COG2151          90 TLSPPWTPDRMSEEAR  105 (111)
T ss_pred             EEECCCCHHHCCHHHH
T ss_conf             9707966554389899


No 6  
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit; InterPro: IPR011883 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA .    .
Probab=98.87  E-value=6.1e-09  Score=71.26  Aligned_cols=73  Identities=11%  Similarity=0.132  Sum_probs=67.3

Q ss_pred             CCCCCCC-CCHHHCCCCCCCCCCCCEEEEE-EEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCC
Q ss_conf             4187999-7623238701013369879999-99672222068999999999985398534069999707898732
Q gi|254780881|r   16 LSIPGEK-NNIVEMQRLSEIFIVHNTVYLS-ITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKNPPQQ   88 (101)
Q Consensus        16 v~dP~~~-~~iv~~g~V~~i~i~~~~v~i~-l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~~~~~   88 (101)
                      |-|||+. -.|++||||+++.++|+-++|. ++-+|.+|+..+.|+++|++||..+.+++.|+|.++-++.|.+.
T Consensus         1 VPDPEiPv~s~~DLGmVR~V~v~g~G~~v~s~tPTySGCPA~~~i~~~i~~A~~~~GW~~~VeV~~~L~P~WTTd   75 (152)
T TIGR02159         1 VPDPEIPVVSVTDLGMVREVEVDGEGVVVKSFTPTYSGCPALEVIRQDIRDALRALGWVEEVEVKTSLDPAWTTD   75 (152)
T ss_pred             CCCCCCCEEEEECCCEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCC
T ss_conf             988887702211065343578647947988874587772368999999999997478975115887718987840


No 7  
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=89.90  E-value=0.94  Score=25.20  Aligned_cols=76  Identities=13%  Similarity=0.166  Sum_probs=60.6

Q ss_pred             CHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCC-CCEEEEEEEECHHHCHHHH-HHHHHHHHHHHC-CCCCCCEEEEEEE
Q ss_conf             589999998414187999762323870101336-9879999996722220689-999999999853-9853406999970
Q gi|254780881|r    5 LKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIV-HNTVYLSITVPHTIAHQLQ-SLRSNAQQIIQN-IPTVKNAVVTLTE   81 (101)
Q Consensus         5 ~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~-~~~v~i~l~l~~~~~~~~~-~l~~~i~~~l~~-i~gv~~v~V~lt~   81 (101)
                      ++++|..+|..=..|.+..+   -|-|+=+.++ ++.+.+.+.=....|++.. .|+.-++++|+. +|+|+.|. .+|-
T Consensus       106 l~~~i~~vl~~ei~P~l~~h---GG~v~lv~i~~~~~v~~~~~G~C~gC~~s~~Tlk~gvE~~l~~~~Pei~~V~-d~td  181 (190)
T TIGR03341       106 LEERINYVLQSEINPQLASH---GGKVTLVEITDDGVAVLQFGGGCNGCSMVDVTLKDGVEKTLLERFPELKGVR-DATD  181 (190)
T ss_pred             HHHHHHHHHHHHCCHHHHHC---CCEEEEEEEECCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEE-ECCC
T ss_conf             99999999986029357636---9989999990797899995754899836899999999999998698753588-7657


Q ss_pred             CCC
Q ss_conf             789
Q gi|254780881|r   82 NKN   84 (101)
Q Consensus        82 ~~~   84 (101)
                      |..
T Consensus       182 h~~  184 (190)
T TIGR03341       182 HTR  184 (190)
T ss_pred             CCC
T ss_conf             888


No 8  
>PRK11190 putative DNA uptake protein; Provisional
Probab=83.23  E-value=3.1  Score=22.24  Aligned_cols=76  Identities=17%  Similarity=0.166  Sum_probs=59.2

Q ss_pred             CHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCC-CCCEEEEEEEECHHHCHHHH-HHHHHHHHHHH-CCCC-CCCEEEEEE
Q ss_conf             58999999841418799976232387010133-69879999996722220689-99999999985-3985-340699997
Q gi|254780881|r    5 LKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFI-VHNTVYLSITVPHTIAHQLQ-SLRSNAQQIIQ-NIPT-VKNAVVTLT   80 (101)
Q Consensus         5 ~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i-~~~~v~i~l~l~~~~~~~~~-~l~~~i~~~l~-~i~g-v~~v~V~lt   80 (101)
                      ++++|...|.+=..|.+..+   -|.|+=+.+ ++|.+.+.+.=...+|++.. .|+.-++..|+ .+|| ++.| +.+|
T Consensus       107 l~~~i~~vl~~~i~P~l~~h---GG~v~l~~i~~~~~~~~~~~G~C~gC~~~~~Tlk~gvE~~l~~~~P~ei~~V-~d~t  182 (192)
T PRK11190        107 LMERVEYVLQSQINPQLAGH---GGRVSLMEITEDGYAILQFGGGCNGCSMVDVTLKEGIEKQLLNEFPGELKGV-RDLT  182 (192)
T ss_pred             HHHHHHHHHHHHCCHHHHHC---CCEEEEEEECCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCEE-EECC
T ss_conf             99999999987319567637---9879999982798899996665789868899999999999998697867057-8766


Q ss_pred             ECCC
Q ss_conf             0789
Q gi|254780881|r   81 ENKN   84 (101)
Q Consensus        81 ~~~~   84 (101)
                      -|..
T Consensus       183 dh~~  186 (192)
T PRK11190        183 EHQR  186 (192)
T ss_pred             CCCC
T ss_conf             6788


No 9  
>pfam01106 NifU NifU-like domain. This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown.
Probab=82.29  E-value=2.2  Score=23.06  Aligned_cols=62  Identities=5%  Similarity=0.017  Sum_probs=45.9

Q ss_pred             HHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHH-HHHHHHHHHHHC-CCCCCCE
Q ss_conf             99984141879997623238701013369879999996722220689-999999999853-9853406
Q gi|254780881|r   10 VDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQ-SLRSNAQQIIQN-IPTVKNA   75 (101)
Q Consensus        10 ~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~-~l~~~i~~~l~~-i~gv~~v   75 (101)
                      .++|.. .-|.+..|   -|-++=+.++++.+.+.|.=.-..|+... .++..+++.|+. +|.+..|
T Consensus         2 ~~~le~-IRP~l~~d---GGdvelv~v~~~~v~v~l~GaC~gC~~s~~Tlk~~Ie~~L~~~vpev~~V   65 (68)
T pfam01106         2 EEVIDE-IRPMLQRD---GGDIELVDVDGDIVKVRLQGACGGCMSSTMTLKGGIERKLRERLGESLRV   65 (68)
T ss_pred             HHHHHH-HCHHHHHC---CCCEEEEEEECCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEE
T ss_conf             779987-56488855---99289999869999999812898981089999999999999878997669


No 10 
>TIGR01748 rhaA L-rhamnose isomerase; InterPro: IPR009308   This family consists of several bacterial L-rhamnose isomerase proteins (5.3.1.14 from EC). This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including Escherichia coli, this is the first step in rhamnose catabolism. Sequential steps are catalyzed by rhamnulose kinase (rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to yield glycerone phosphate and (S)-lactaldehyde. ; GO: 0008740 L-rhamnose isomerase activity, 0030145 manganese ion binding, 0019299 rhamnose metabolic process.
Probab=82.15  E-value=2.1  Score=23.19  Aligned_cols=71  Identities=11%  Similarity=0.028  Sum_probs=48.2

Q ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEE--ECHHH-CHHHHHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf             999998414187999762323870101336987999999--67222-206899999999998539853406999
Q gi|254780881|r    8 QIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSIT--VPHTI-AHQLQSLRSNAQQIIQNIPTVKNAVVT   78 (101)
Q Consensus         8 ~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~--l~~~~-~~~~~~l~~~i~~~l~~i~gv~~v~V~   78 (101)
                      +|.+||++..+=-..-==..-+=|++-...+|.++=.|.  =+||+ +...++|+++.|+|++=|||-..++.-
T Consensus        18 DvEeALr~L~~~piS~HCWQGDDv~GFenp~GeLtGGI~aTGNYPGkA~tp~eLR~DLEkA~sLIPGk~rlNLH   91 (415)
T TIGR01748        18 DVEEALRQLEDVPISMHCWQGDDVEGFENPEGELTGGIDATGNYPGKARTPEELRRDLEKALSLIPGKHRLNLH   91 (415)
T ss_pred             CHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCEECCEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             67898864165865676314876454256886312561012588856689788889999997508898510115


No 11 
>pfam09650 PHA_gran_rgn Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn). Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins found at the surface of PHA granules. These proteins have so far been found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.
Probab=79.71  E-value=3  Score=22.34  Aligned_cols=45  Identities=0%  Similarity=0.118  Sum_probs=38.9

Q ss_pred             HHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCC
Q ss_conf             232387010133698799999967222206899999999998539
Q gi|254780881|r   25 IVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNI   69 (101)
Q Consensus        25 iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i   69 (101)
                      +--.|.-..+.+.++.+.+.+.|+.-..++...|+++|++.|-++
T Consensus        42 F~~~Gv~G~l~v~~~~v~v~i~Lg~ll~~fkg~Ie~eIe~~LD~~   86 (87)
T pfam09650        42 FKRSGVKGTLHVTEDKIRVDLKLGFLLSAFKGRIEQEIEKNLDKL   86 (87)
T ss_pred             EEECCCCEEEEECCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             971775469998277799999928888876768999999988721


No 12 
>TIGR02830 spore_III_AG stage III sporulation protein AG; InterPro: IPR014195    This entry represents the stage III sporulation protein AG, which is encoded in a spore formation operon: spoIIIAABCDEFGH under the control of sigma G . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species..
Probab=79.69  E-value=3.2  Score=22.16  Aligned_cols=34  Identities=12%  Similarity=0.239  Sum_probs=28.5

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCC
Q ss_conf             2068999999999985398534069999707898
Q gi|254780881|r   52 AHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKNP   85 (101)
Q Consensus        52 ~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~~   85 (101)
                      ..+..++..+.+++|.+|.||.+|+|.++.....
T Consensus        62 ~~yE~~~e~~Lk~~Le~I~GVg~V~V~vnL~~~e   95 (193)
T TIGR02830        62 SDYEKEYENELKEILEKIEGVGDVTVMVNLDSSE   95 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCC
T ss_conf             9999999999999864203756148999965996


No 13 
>COG5133 Uncharacterized conserved protein [Function unknown]
Probab=78.76  E-value=6  Score=20.65  Aligned_cols=77  Identities=13%  Similarity=0.141  Sum_probs=57.7

Q ss_pred             CCHHHHHHHHHHCCCCCCCCCHHHCCCC--CCCCCCCC-------EEEEEEEECHHHCHHHHHHHHHHHHHHHC-CCCCC
Q ss_conf             3589999998414187999762323870--10133698-------79999996722220689999999999853-98534
Q gi|254780881|r    4 ILKNQIVDSLKVLSIPGEKNNIVEMQRL--SEIFIVHN-------TVYLSITVPHTIAHQLQSLRSNAQQIIQN-IPTVK   73 (101)
Q Consensus         4 ~~~~~I~~~L~~v~dP~~~~~iv~~g~V--~~i~i~~~-------~v~i~l~l~~~~~~~~~~l~~~i~~~l~~-i~gv~   73 (101)
                      ++.+.|.+.+..|.||+-...+-.++.|  +++++.+|       -|.+.++-+-|.|.+..-+.--|+-.|+. +|---
T Consensus        54 id~qeiydLia~I~DPEHPltL~QLsVV~lEdi~v~D~~~~n~i~~v~v~itPTIpHCSmatlIGLcIrvrleR~lpprF  133 (181)
T COG5133          54 IDQQEIYDLIADIRDPEHPLTLEQLSVVSLEDISVPDGIAPNVIRCVKVVITPTIPHCSMATLIGLCIRVRLERHLPPRF  133 (181)
T ss_pred             CCHHHHHHHHHHCCCCCCCCCHHHCCEEEECCCCCCCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHEEEEEHHCCCCCE
T ss_conf             68899999998607988874076601352025534678887704789999635887206887764320332000379841


Q ss_pred             CEEEEEE
Q ss_conf             0699997
Q gi|254780881|r   74 NAVVTLT   80 (101)
Q Consensus        74 ~v~V~lt   80 (101)
                      .|+|.+.
T Consensus       134 ~v~v~ik  140 (181)
T COG5133         134 HVQVHIK  140 (181)
T ss_pred             EEEEEEE
T ss_conf             6899981


No 14 
>KOG3381 consensus
Probab=74.01  E-value=6  Score=20.64  Aligned_cols=77  Identities=12%  Similarity=0.108  Sum_probs=57.0

Q ss_pred             CHHHHHHHHHHCCCCCCCCCHHHCCCCCC--CCCCC-------CEEEEEEEECHHHCHHHHHHHHHHHHHHH-CCCCCCC
Q ss_conf             58999999841418799976232387010--13369-------87999999672222068999999999985-3985340
Q gi|254780881|r    5 LKNQIVDSLKVLSIPGEKNNIVEMQRLSE--IFIVH-------NTVYLSITVPHTIAHQLQSLRSNAQQIIQ-NIPTVKN   74 (101)
Q Consensus         5 ~~~~I~~~L~~v~dP~~~~~iv~~g~V~~--i~i~~-------~~v~i~l~l~~~~~~~~~~l~~~i~~~l~-~i~gv~~   74 (101)
                      ..+.+.+.++.|.||+-...+-+++-|+.  +++.+       ..|.+.++-+-|.|.+.--|---|+-.|. .+|---+
T Consensus        35 ~~~~~~dlir~I~DPEhP~TLeqL~VV~ee~v~V~d~~~~~~~s~V~i~ftPTipHCSmaTlIGLcIrVkl~RsLp~rfk  114 (161)
T KOG3381          35 DAEEIFDLIRDIRDPEHPLTLEQLNVVSEEGVEVDDPNVGDEESYVRITFTPTIPHCSMATLIGLCIRVKLLRSLPPRFK  114 (161)
T ss_pred             HHHHHHHHHHCCCCCCCCCCHHHCCCEEECCEEEECCCCCCCCEEEEEEECCCCCCCHHHHHHHHEEEEEEEECCCCCEE
T ss_conf             67899999861689888865887062422056764577788513899995368875227766422026655304887426


Q ss_pred             EEEEEEE
Q ss_conf             6999970
Q gi|254780881|r   75 AVVTLTE   81 (101)
Q Consensus        75 v~V~lt~   81 (101)
                      +.|.++.
T Consensus       115 vdV~I~~  121 (161)
T KOG3381         115 VDVYIKP  121 (161)
T ss_pred             EEEEECC
T ss_conf             8999757


No 15 
>TIGR01608 citD citrate lyase acyl carrier protein; InterPro: IPR006495    This group of sequences represent the acyl carrier protein (gamma subunit) of the holoenzyme citrate lyase (4.1.3.6 from EC) composed of alpha (2.8.3.10 from EC), beta (4.1.3.34 from EC), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The acyl carrier protein covalently binds the coenzyme of citrate lyase. The set contains an experimentally characterised member from Leuconostoc mesenteroides . The sequences come from a wide range of Gram-positive bacteria. For Gram-negative bacteria, it appears that only sequences from the gamma proteobacteria are included..
Probab=70.99  E-value=8.2  Score=19.90  Aligned_cols=46  Identities=15%  Similarity=0.278  Sum_probs=34.5

Q ss_pred             CCCCCC-EEEEEEEECHHH-CHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             133698-799999967222-20689999999999853985340699997
Q gi|254780881|r   34 IFIVHN-TVYLSITVPHTI-AHQLQSLRSNAQQIIQNIPTVKNAVVTLT   80 (101)
Q Consensus        34 i~i~~~-~v~i~l~l~~~~-~~~~~~l~~~i~~~l~~i~gv~~v~V~lt   80 (101)
                      |.+..+ ..+|.|.+.+.= ..+...|+.-+++.|..+ ||+++.|.+.
T Consensus        19 v~v~pa~~~Gi~~~l~S~VkkQFg~~I~~~vkeTL~~l-Gv~~a~v~v~   66 (95)
T TIGR01608        19 VSVEPAAQVGIEIDLSSSVKKQFGDEIEKVVKETLKEL-GVENAVVKVV   66 (95)
T ss_pred             EEECCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEEE
T ss_conf             77324888847887520177775799999999989865-9443568872


No 16 
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=60.00  E-value=6.5  Score=20.44  Aligned_cols=26  Identities=23%  Similarity=0.388  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHCCCCCCCEEEEEEECC
Q ss_conf             99999999853985340699997078
Q gi|254780881|r   58 LRSNAQQIIQNIPTVKNAVVTLTENK   83 (101)
Q Consensus        58 l~~~i~~~l~~i~gv~~v~V~lt~~~   83 (101)
                      =...++++|++++||.++.|.+..++
T Consensus        12 C~~~Ie~~l~~~~GV~~~~vn~~~~~   37 (63)
T cd00371          12 CVSKIEKALEKLPGVESVEVDLETGK   37 (63)
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCE
T ss_conf             99999999707999579999888999


No 17 
>TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A; InterPro: IPR013485    This entry consists of archaeal proteins which are predicted to be functionally equivalent to MoaA (molybdenum cofactor biosynthesis protein A) from bacteria (see IPR013483 from INTERPRO).; GO: 0046872 metal ion binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=57.36  E-value=18  Score=17.99  Aligned_cols=78  Identities=9%  Similarity=0.153  Sum_probs=57.9

Q ss_pred             CCHHHHHHHHHHCCCCCC-CCCHHHCCCC-----CCCCCCC-CEEEEEEEECHH---------HCHHHHHHHHHHHHHHH
Q ss_conf             358999999841418799-9762323870-----1013369-879999996722---------22068999999999985
Q gi|254780881|r    4 ILKNQIVDSLKVLSIPGE-KNNIVEMQRL-----SEIFIVH-NTVYLSITVPHT---------IAHQLQSLRSNAQQIIQ   67 (101)
Q Consensus         4 ~~~~~I~~~L~~v~dP~~-~~~iv~~g~V-----~~i~i~~-~~v~i~l~l~~~---------~~~~~~~l~~~i~~~l~   67 (101)
                      +++.+|.++.+.+++-.. .-++..-|..     +++.-.| ++|.|+|....+         .....+....-|++|+.
T Consensus        74 lLR~D~~~Ii~~~~~~~~~~vSmTTNG~LL~~~A~~Lk~AGLdRVNVSLdtld~e~Y~kITG~~~~~~~~Vi~GI~~A~~  153 (324)
T TIGR02668        74 LLRKDLIEIIRRIKDYGIKDVSMTTNGILLEKLAKKLKEAGLDRVNVSLDTLDPEKYKKITGQSRDALDRVIEGIESAVD  153 (324)
T ss_pred             CHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             34566999998614675034420303144898999999828561312026788678886448998607899999999997


Q ss_pred             CCCCCCCEEEEEEECC
Q ss_conf             3985340699997078
Q gi|254780881|r   68 NIPTVKNAVVTLTENK   83 (101)
Q Consensus        68 ~i~gv~~v~V~lt~~~   83 (101)
                      .  |...|+++++.-+
T Consensus       154 ~--GL~PVKlN~Vvl~  167 (324)
T TIGR02668       154 A--GLTPVKLNMVVLK  167 (324)
T ss_pred             C--CCCCEEEEEEEEC
T ss_conf             2--8981378888754


No 18 
>pfam00403 HMA Heavy-metal-associated domain.
Probab=56.67  E-value=8.7  Score=19.74  Aligned_cols=26  Identities=15%  Similarity=0.333  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHCCCCCCCEEEEEEEC
Q ss_conf             99999999985398534069999707
Q gi|254780881|r   57 SLRSNAQQIIQNIPTVKNAVVTLTEN   82 (101)
Q Consensus        57 ~l~~~i~~~l~~i~gv~~v~V~lt~~   82 (101)
                      .=...++++|.++|||.++.+.+..+
T Consensus        11 ~C~~~Ie~~l~~~~GV~~v~v~~~~~   36 (62)
T pfam00403        11 GCAKKVEKALSKLPGVSSVSVDLETG   36 (62)
T ss_pred             HHHHHHHHHHHCCCCCEEEEEECCCC
T ss_conf             99999999985599954999987899


No 19 
>TIGR01162 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit; InterPro: IPR000031   Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain . The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex.
Probab=48.48  E-value=25  Score=17.17  Aligned_cols=44  Identities=14%  Similarity=0.240  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCC------CCCCC-CEEEEEC
Q ss_conf             999999999853985340699997078987321------56998-5588859
Q gi|254780881|r   57 SLRSNAQQIIQNIPTVKNAVVTLTENKNPPQQR------NNLNV-KKFVAVA  101 (101)
Q Consensus        57 ~l~~~i~~~l~~i~gv~~v~V~lt~~~~~~~~~------~~~gv-KnIIAVA  101 (101)
                      ...+.+-+.|+.| ||.-.--+..+||+|..-.      .-.|+ |=|||+|
T Consensus        12 ~~m~~a~~~L~~f-gi~~e~~V~SAHRTP~~~~~ya~~a~~~G~P~ViIAgA   62 (159)
T TIGR01162        12 ETMKKAAEILEEF-GIPYELRVVSAHRTPELMFEYAKEAEERGIPKVIIAGA   62 (159)
T ss_pred             HHHHHHHHHHHHC-CCCEEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             8999999999855-99667898606778088999999998678997998403


No 20 
>pfam03780 DUF322 Protein of unknown function (DUF322). This is a family of small proteins. It includes a protein identified as an alkaline shock protein so may be involved in stress response.
Probab=47.62  E-value=26  Score=17.09  Aligned_cols=43  Identities=9%  Similarity=0.222  Sum_probs=31.8

Q ss_pred             CCEEEEE----EEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             9879999----996722220689999999999853985340699997
Q gi|254780881|r   38 HNTVYLS----ITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLT   80 (101)
Q Consensus        38 ~~~v~i~----l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt   80 (101)
                      ++.+.++    +..+.+-....+.++..++++++.+.|++-..|.+.
T Consensus        57 ~~~v~v~l~v~v~YG~~i~~v~~~iq~~V~~~v~~mtgl~V~~VnV~  103 (108)
T pfam03780        57 EGQVAIDLYVIVEYGVNIPEVAKNIQEKVKYAVENMTGLEVSEVNVH  103 (108)
T ss_pred             CCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCEEEEEEEE
T ss_conf             98699999999977998899999999999999999879867899999


No 21 
>TIGR02052 MerP mercuric transport protein periplasmic component; InterPro: IPR011795    This entry represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding . MerP is related to a larger family of metal binding proteins.; GO: 0015097 mercury ion transmembrane transporter activity, 0045340 mercury ion binding, 0015694 mercury ion transport, 0046689 response to mercury ion, 0042597 periplasmic space.
Probab=46.66  E-value=9  Score=19.67  Aligned_cols=32  Identities=16%  Similarity=0.283  Sum_probs=24.9

Q ss_pred             EEEEEECHH---HCHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             999996722---22068999999999985398534069999
Q gi|254780881|r   42 YLSITVPHT---IAHQLQSLRSNAQQIIQNIPTVKNAVVTL   79 (101)
Q Consensus        42 ~i~l~l~~~---~~~~~~~l~~~i~~~l~~i~gv~~v~V~l   79 (101)
                      +|.|++|+-   .||+-      ++.||+++|||++++|.+
T Consensus        24 TVTL~vPgMtC~aCPiT------V~~AL~kVdGV~Kaev~f   58 (92)
T TIGR02052        24 TVTLEVPGMTCAACPIT------VKTALKKVDGVEKAEVDF   58 (92)
T ss_pred             CEEEECCCCCCCCCCHH------HHHHCCCCCCCCCEEEEC
T ss_conf             33530688866678501------774064388800000012


No 22 
>TIGR03123 one_C_unchar_1 probable H4MPT-linked C1 transfer pathway protein. This protein family was identified, by the method of partial phylogenetic profiling, as related to the use of tetrahydromethanopterin (H4MPT) as a C-1 carrier. Characteristic markers of the H4MPT-linked C1 transfer pathway include formylmethanofuran dehydrogenase subunits, methenyltetrahydromethanopterin cyclohydrolase, etc. Tetrahydromethanopterin, a tetrahydrofolate analog, occurs in methanogenic archaea, bacterial methanotrophs, planctomycetes, and a few other lineages.
Probab=41.95  E-value=12  Score=19.01  Aligned_cols=47  Identities=15%  Similarity=0.153  Sum_probs=34.7

Q ss_pred             CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCC
Q ss_conf             98799999967222206899999999998539853406999970789
Q gi|254780881|r   38 HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKN   84 (101)
Q Consensus        38 ~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~   84 (101)
                      +|.+.-.-..+.|-....+.|...+++....++....+-|.||.+-.
T Consensus        18 ~g~i~~~~~~~~plWk~~~~L~~~l~~i~~~~~~~~~~avTMTgELa   64 (318)
T TIGR03123        18 DGRIKEVHQLYCPLWKGNDKLAETLKEISQDLSSADNVAVTMTGELA   64 (318)
T ss_pred             CCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEHHHH
T ss_conf             98688999851702178367899999999855831318999206576


No 23 
>pfam08921 DUF1904 Domain of unknown function (DUF1904). This domain is found in a set of hypothetical bacterial proteins.
Probab=41.83  E-value=32  Score=16.57  Aligned_cols=73  Identities=5%  Similarity=0.129  Sum_probs=53.5

Q ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEE-----EEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEC
Q ss_conf             99999841418799976232387010133698799-----9999672222068999999999985398534069999707
Q gi|254780881|r    8 QIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVY-----LSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTEN   82 (101)
Q Consensus         8 ~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~-----i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~   82 (101)
                      .+.+.|..+.  ..+++-+.+.++....+.+|.+.     |.+.-=.-+.+..+.+.+-|.+.++.++|-.+|.|.++.=
T Consensus        19 ~Li~eLa~i~--~~~~e~ftlE~i~s~~~~~G~~~~~ypfVEVlWF~R~qe~~d~vA~~It~~v~~~~~~~~V~V~F~~L   96 (107)
T pfam08921        19 TLIEELADIC--KCPPEAFTLEWINSVFFRDGKIDDAYPFVEVLWFPRDQETQDLVAQIITEAVRAVNGLQDVAVIFTAL   96 (107)
T ss_pred             HHHHHHHHHH--CCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC
T ss_conf             9999999997--79824489998336899737556773359999803898999999999999998438997399999964


No 24 
>pfam04953 consensus
Probab=40.93  E-value=33  Score=16.48  Aligned_cols=38  Identities=11%  Similarity=0.156  Sum_probs=28.6

Q ss_pred             EEEEEECHH-HCHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             999996722-220689999999999853985340699997
Q gi|254780881|r   42 YLSITVPHT-IAHQLQSLRSNAQQIIQNIPTVKNAVVTLT   80 (101)
Q Consensus        42 ~i~l~l~~~-~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt   80 (101)
                      .+.+++.+. ...+-++|+.-+++.|..+ ||+++.|.+.
T Consensus        28 gi~iel~S~V~kQFG~~Ir~~v~etL~~l-gV~~a~v~v~   66 (97)
T pfam04953        28 GIELELDSSVEKQFGDAIRQTIRETLAAY-GVTAAQVNVV   66 (97)
T ss_pred             CEEEEEEEHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEEE
T ss_conf             56999977899997699999999999983-9734799997


No 25 
>cd00756 MoaE MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits.
Probab=40.13  E-value=34  Score=16.41  Aligned_cols=67  Identities=7%  Similarity=0.013  Sum_probs=44.5

Q ss_pred             HHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf             9999841418799976232387010133698799999967222206899999999998539853406999
Q gi|254780881|r    9 IVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVT   78 (101)
Q Consensus         9 I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~   78 (101)
                      +...+..+.+|+.|--..-.|.|++-.  +|.-.-.|++.........+|++-++++.... ++..+.+.
T Consensus         3 ~~~~~~~~~~~~~GAiv~F~G~VR~~~--~g~~v~~L~ye~y~~mA~k~l~~I~~~~~~k~-~i~~v~i~   69 (124)
T cd00756           3 LAELLAALRDPEAGAVVTFVGTVRDHD--EGKGVEALEYEAYPPMAEKELEEIAEEARERW-GLLRVAII   69 (124)
T ss_pred             HHHHHHHHCCCCCCEEEEEEEEECCCC--CCCCEEEEEEEEECHHHHHHHHHHHHHHHHCC-CCCEEEEE
T ss_conf             899999726989986999999978899--99633179999600678999999999998507-87608999


No 26 
>TIGR02610 PHA_gran_rgn putative polyhydroxyalkanoic acid system protein; InterPro: IPR013433    Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria..
Probab=38.06  E-value=27  Score=16.95  Aligned_cols=47  Identities=4%  Similarity=0.132  Sum_probs=40.5

Q ss_pred             CCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHC
Q ss_conf             97623238701013369879999996722220689999999999853
Q gi|254780881|r   22 KNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQN   68 (101)
Q Consensus        22 ~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~   68 (101)
                      .-+|-=.|.=..|.+-+..|.|+++|..--..+...++.+|+++|-.
T Consensus        42 tl~~aRsGv~Gav~~g~~~irv~~eLG~llSaM~g~iksEI~raLdk   88 (91)
T TIGR02610        42 TLRIARSGVDGAVHLGEESIRVEVELGMLLSAMSGTIKSEIERALDK   88 (91)
T ss_pred             EEEEEECCCCCEEEECCCEEEEEEEECHHHHHCCCCCHHHHHHHHHH
T ss_conf             66777516773364278416886310116530287536889999886


No 27 
>COG4806 RhaA L-rhamnose isomerase [Carbohydrate transport and metabolism]
Probab=37.27  E-value=38  Score=16.15  Aligned_cols=71  Identities=14%  Similarity=0.073  Sum_probs=46.1

Q ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEE--ECHHH-CHHHHHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf             999998414187999762323870101336987999999--67222-206899999999998539853406999
Q gi|254780881|r    8 QIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSIT--VPHTI-AHQLQSLRSNAQQIIQNIPTVKNAVVT   78 (101)
Q Consensus         8 ~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~--l~~~~-~~~~~~l~~~i~~~l~~i~gv~~v~V~   78 (101)
                      ++.++|++..+--..---..-+-|++.+..+|.++=.+.  -+||+ +...++++++.+.||+-+||-..++..
T Consensus        22 Dve~AL~~L~~~piSmHCWQGDDv~GFe~~~GeLtGGI~~TGnYPGkA~t~~eLR~DLEkAlsLIPG~~rlNLH   95 (419)
T COG4806          22 DVEEALRQLDRLPVSMHCWQGDDVSGFENPEGELTGGIQATGNYPGKARNAEELRADLEKALSLIPGPKRLNLH   95 (419)
T ss_pred             CHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCEEECCEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             69999988741862666405786556147887041554404778876699899999999987408896513236


No 28 
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=37.24  E-value=25  Score=17.17  Aligned_cols=42  Identities=14%  Similarity=0.146  Sum_probs=28.0

Q ss_pred             CEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC
Q ss_conf             879999996722220689999999999853985340699997078
Q gi|254780881|r   39 NTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENK   83 (101)
Q Consensus        39 ~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~   83 (101)
                      +..+.+..+..-.|..   =...+|++|.++|||.+++|.++.++
T Consensus        47 ~~~~~~f~V~GM~Caa---Ca~~IE~~L~~~~GV~~a~Vn~at~~   88 (739)
T PRK11033         47 SGTRYSWKVSGMDCPS---CARKVENAVRQLAGVNQAQVLFATEK   88 (739)
T ss_pred             CCCEEEEEECCCCCHH---HHHHHHHHHHCCCCEEEEEEECCCCE
T ss_conf             7867579977844699---99999998717979339999976878


No 29 
>COG3965 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=36.37  E-value=39  Score=16.07  Aligned_cols=39  Identities=10%  Similarity=0.113  Sum_probs=31.7

Q ss_pred             CHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCC
Q ss_conf             722220689999999999853985340699997078987
Q gi|254780881|r   48 PHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKNPP   86 (101)
Q Consensus        48 ~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~~~   86 (101)
                      +.-.-+.++++++++.++|...+-=.-+++.+|.+++|.
T Consensus       275 ~ar~Ved~d~Irdei~~slg~~g~~rwltvsfT~D~kWa  313 (314)
T COG3965         275 DARNVEDWDDIRDEIGQSLGSLGYERWLTVSFTRDEKWA  313 (314)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC
T ss_conf             874633689999999888634786743899985330003


No 30 
>PRK13253 citrate lyase subunit gamma; Provisional
Probab=34.41  E-value=42  Score=15.89  Aligned_cols=41  Identities=12%  Similarity=0.173  Sum_probs=31.0

Q ss_pred             CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             9879999996722220689999999999853985340699997
Q gi|254780881|r   38 HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLT   80 (101)
Q Consensus        38 ~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt   80 (101)
                      +|.+.+.|+-. ....+-++|+.-+++.|..+ ||+++.|.+.
T Consensus        26 ~g~i~i~l~S~-V~kQFG~~Ir~~v~etL~~l-gV~~~~v~v~   66 (92)
T PRK13253         26 TQGIDIQLESS-VEKQFGDQIRAVILETLAKL-GVTNAQVNVD   66 (92)
T ss_pred             CCCEEEEEEEH-HHHHHHHHHHHHHHHHHHHC-CCCEEEEEEE
T ss_conf             98379999678-99987799999999999972-9751699995


No 31 
>TIGR00884 guaA_Cterm GMP synthase, C-terminal domain; InterPro: IPR001674   The amidotransferase family of enzymes utilises the ammonia derived from the hydrolysis of glutamine for a subsequent chemical reaction catalyzed by the same enzyme. The ammonia intermediate does not dissociate into solution during the chemical transformations . GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. The C-terminal domain is specific to the GMP synthases 6.3.5.2 from EC. In prokaryotes this domain mediates dimerisation. Eukaryotic GMP synthases are monomers. This domain in eukaryotes includes several large insertions that may form globular domains .; GO: 0003922 GMP synthase (glutamine-hydrolyzing) activity, 0005524 ATP binding, 0006164 purine nucleotide biosynthetic process, 0006177 GMP biosynthetic process.
Probab=33.32  E-value=18  Score=17.95  Aligned_cols=30  Identities=20%  Similarity=0.333  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHCCCCCCCEEEEEEECCC
Q ss_conf             899999999998539853406999970789
Q gi|254780881|r   55 LQSLRSNAQQIIQNIPTVKNAVVTLTENKN   84 (101)
Q Consensus        55 ~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~   84 (101)
                      |+-|++=..+....+++|+.|-..+|+.++
T Consensus       284 yd~L~ris~RItnEv~~V~RVVYDITsKPP  313 (319)
T TIGR00884       284 YDLLERISNRITNEVPGVNRVVYDITSKPP  313 (319)
T ss_pred             HHHHHHHHCCCCCCCCCCEEEEEEECCCCC
T ss_conf             889988821100122884079985167349


No 32 
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family; InterPro: IPR003282 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia.   The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell  and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.    One of the outer membrane protein subunit families, termed "K" here for nomenclature purposes, aids in the structural assembly of the invasion complex . It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.; GO: 0009306 protein secretion.
Probab=32.30  E-value=46  Score=15.68  Aligned_cols=67  Identities=24%  Similarity=0.310  Sum_probs=43.0

Q ss_pred             HHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECH-HHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCC
Q ss_conf             99998414187999762323870101336987999999672-22206899999999998539853406999970789
Q gi|254780881|r    9 IVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPH-TIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKN   84 (101)
Q Consensus         9 I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~-~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~   84 (101)
                      -++.|+..-.|.-.     ..-+.+++-.+|-|.    -|. ..+.+.=.+.+++++.|+.++||-++.|.+..+..
T Consensus        75 A~~lL~~~GLP~~~-----~~~~~~~Fp~~gLvs----SP~eEraR~~ya~eQ~Le~tLs~IdGV~~ArVhVvlP~~  142 (203)
T TIGR02544        75 AVELLRQNGLPRQS-----FVNLGELFPKDGLVS----SPTEERARLLYAIEQELEQTLSQIDGVISARVHVVLPEN  142 (203)
T ss_pred             HHHHHHHCCCCCCC-----CCCHHHHCCCCCEEC----CHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCC
T ss_conf             99999863888953-----236887513577034----869999999999999999986017926866799972167


No 33 
>PRK10671 copA copper exporting ATPase; Provisional
Probab=29.87  E-value=50  Score=15.45  Aligned_cols=40  Identities=20%  Similarity=0.233  Sum_probs=28.7

Q ss_pred             EEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC
Q ss_conf             9999996722220689999999999853985340699997078
Q gi|254780881|r   41 VYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTENK   83 (101)
Q Consensus        41 v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~   83 (101)
                      -.+.|.+..-.|..   -...+|++|+++|||.+++|.+..++
T Consensus        99 ~~~~l~i~Gm~Caa---C~~~ie~~l~~~~GV~~a~Vn~~~~~  138 (834)
T PRK10671         99 DSQQLLLSGMSCAS---CVTRVQNALQSVPGVTQARVNLAERT  138 (834)
T ss_pred             CEEEEEECCCCHHH---HHHHHHHHHHCCCCEEEEEEECCCCE
T ss_conf             55899987835288---89999999836979008999988883


No 34 
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=29.62  E-value=51  Score=15.42  Aligned_cols=18  Identities=17%  Similarity=0.202  Sum_probs=7.4

Q ss_pred             HHHHHHHHCCCCCCCEEE
Q ss_conf             999999853985340699
Q gi|254780881|r   60 SNAQQIIQNIPTVKNAVV   77 (101)
Q Consensus        60 ~~i~~~l~~i~gv~~v~V   77 (101)
                      ..++..|+.+|||..|.+
T Consensus       169 ~~l~~~L~~i~GV~~V~i  186 (1040)
T PRK10503        169 TRVAQKISQVSGVGLVTL  186 (1040)
T ss_pred             HHHHHHHHCCCCEEEEEE
T ss_conf             999999847999179997


No 35 
>PRK05783 hypothetical protein; Provisional
Probab=27.10  E-value=57  Score=15.16  Aligned_cols=65  Identities=14%  Similarity=0.090  Sum_probs=42.3

Q ss_pred             HHCCCCCC---CCCHHHCCCCCCCCCC-CCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             41418799---9762323870101336-987999999672222068999999999985398534069999
Q gi|254780881|r   14 KVLSIPGE---KNNIVEMQRLSEIFIV-HNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL   79 (101)
Q Consensus        14 ~~v~dP~~---~~~iv~~g~V~~i~i~-~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l   79 (101)
                      .++.||+.   .++++..|+-+-..+. |..+.|.++-+.+. ...+.....|.+....=|=|..++|.+
T Consensus        13 ~gi~DPeG~TI~~~L~~~g~~~v~~vR~GK~l~~~iea~s~e-eA~~~v~~ic~~lrL~NPvI~~~~i~v   81 (84)
T PRK05783         13 DGIRDPEGETIQRYVLERMLGYSIEVRAGKCLVFRIEASSPE-EAQELALKLAKEMRLGNPIVHKIVVRV   81 (84)
T ss_pred             CCCCCCCHHHHHHHHHHHCCCCEEEEEEEEEEEEEEECCCHH-HHHHHHHHHHHHHHCCCCCEEEEEEEE
T ss_conf             977596337999999985589648987104999999479989-999999999986203498528999999


No 36 
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=27.00  E-value=57  Score=15.15  Aligned_cols=43  Identities=21%  Similarity=0.305  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHCCCCCCCEEEEEEECCCCCCC------CCCCCCCEEEEEC
Q ss_conf             9999999985398534069999707898732------1569985588859
Q gi|254780881|r   58 LRSNAQQIIQNIPTVKNAVVTLTENKNPPQQ------RNNLNVKKFVAVA  101 (101)
Q Consensus        58 l~~~i~~~l~~i~gv~~v~V~lt~~~~~~~~------~~~~gvKnIIAVA  101 (101)
                      ..+.+-+.|..+ ||.-..-.+.+|+.|..-      -.-.|+|-|||.|
T Consensus        17 ~mk~Aa~~L~~f-gv~ye~~VvSAHRTPe~m~~ya~~a~~~g~~viIAgA   65 (162)
T COG0041          17 TMKKAAEILEEF-GVPYEVRVVSAHRTPEKMFEYAEEAEERGVKVIIAGA   65 (162)
T ss_pred             HHHHHHHHHHHC-CCCEEEEEEECCCCHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             999999999984-9975999984467989999999999878975999657


No 37 
>pfam01251 Ribosomal_S7e Ribosomal protein S7e.
Probab=26.65  E-value=58  Score=15.12  Aligned_cols=73  Identities=16%  Similarity=0.176  Sum_probs=50.8

Q ss_pred             CHHHHHHHHHHCC--CCCCCCCHHHCCC--CCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHC-CCCCCCEEE
Q ss_conf             5899999984141--8799976232387--01013369879999996722220689999999999853-985340699
Q gi|254780881|r    5 LKNQIVDSLKVLS--IPGEKNNIVEMQR--LSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQN-IPTVKNAVV   77 (101)
Q Consensus         5 ~~~~I~~~L~~v~--dP~~~~~iv~~g~--V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~-i~gv~~v~V   77 (101)
                      .+++|-++|-.+.  .|++..++-++-.  ++++++.+|.=.+.+.+|++....+..+....-..|+. +.|-.-+.|
T Consensus        14 ~E~~Vaqal~dLE~~~~dLK~~Lr~L~i~~akEi~v~~gkKaivIfVP~p~lk~f~Kiq~rLvrELEKKfsgkhVv~i   91 (189)
T pfam01251        14 LELSVAQALFDLESNSPDLKAELRDLQITSAKEIEVGGGKKAVVIFVPVPQLKAYRKIQQRLVRELEKKFSGKHVVFV   91 (189)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHCEEEEEEEEEECCCCEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             999999999999827798987634028855699985699479999960799899999999999999864589879999


No 38 
>pfam01514 YscJ_FliF Secretory protein of YscJ/FliF family. This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins.
Probab=25.70  E-value=60  Score=15.01  Aligned_cols=33  Identities=18%  Similarity=0.216  Sum_probs=26.1

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCC
Q ss_conf             206899999999998539853406999970789
Q gi|254780881|r   52 AHQLQSLRSNAQQIIQNIPTVKNAVVTLTENKN   84 (101)
Q Consensus        52 ~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~~~~   84 (101)
                      ......+..++++.|..++||.++.|.++-++.
T Consensus       109 ~~~~rAle~eL~rtI~~i~gV~~ArVhl~lPe~  141 (206)
T pfam01514       109 ARLIYALEQELSRTLSQIDGVISARVHIVLPER  141 (206)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCC
T ss_conf             999999999999999727883067999967887


No 39 
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=25.62  E-value=60  Score=15.01  Aligned_cols=68  Identities=13%  Similarity=0.191  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCC--EEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             0358999999841418799976232387010133698--79999996722220689999999999853985340699997
Q gi|254780881|r    3 QILKNQIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHN--TVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLT   80 (101)
Q Consensus         3 ~~~~~~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~--~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt   80 (101)
                      +...+.+.+.++.....+..     .+.+..--+.=|  .+.+.+..+-     .+...+.+++++++++||.++.|.-.
T Consensus        16 evDle~L~e~ik~~l~~~~~-----i~~~e~ePiAFGLkaL~v~vv~~D-----~eG~tD~~Ee~~~~iegV~sveV~~v   85 (88)
T PRK00435         16 EVDLDELKEKIKEKLPEGYE-----INRIEEEPIAFGLKALKLYVIMPD-----EEGGTDPVEEAFAAVEGVESVEVEEV   85 (88)
T ss_pred             CCCHHHHHHHHHHHCCCCCE-----EEEEEEEEEECCCEEEEEEEEEEC-----CCCCCHHHHHHHHCCCCCCEEEEEEE
T ss_conf             86999999999975758764-----746678845645232799999975-----88683799999854689657999988


No 40 
>TIGR00003 TIGR00003 copper ion binding protein; InterPro: IPR006122    Proteins that transport heavy metals in micro-organisms and eukaryotes share similarities in their sequences and structures.    These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases .    A conserved 30-residue domain has been found in a number of these heavy metal transport or detoxification proteins . The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. This sub-domain is found in copper-binding proteins. ; GO: 0005507 copper ion binding, 0006825 copper ion transport.
Probab=25.58  E-value=43  Score=15.82  Aligned_cols=27  Identities=15%  Similarity=0.241  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHCCCCCCCEEEEEEECC
Q ss_conf             999999999853985340699997078
Q gi|254780881|r   57 SLRSNAQQIIQNIPTVKNAVVTLTENK   83 (101)
Q Consensus        57 ~l~~~i~~~l~~i~gv~~v~V~lt~~~   83 (101)
                      .=-+.||+.+..|+||+.+.|.|...+
T Consensus        13 HCV~~iE~~VGel~GVs~v~v~L~k~~   39 (66)
T TIGR00003        13 HCVDKIEKFVGELEGVSAVKVQLEKEK   39 (66)
T ss_pred             HHHHHHHHHCCEECCCEEEEEEEECCE
T ss_conf             247765410470037306766763241


No 41 
>TIGR01923 menE O-succinylbenzoate-CoA ligase; InterPro: IPR010192   This entry represents the enzyme O-succinylbenzoate-CoA ligase (MenE), which is involved in the fourth step of the menaquinone (vitamin K2) biosynthesis pathway. In bacteria, menaquinone is used during fumarate reduction in anaerobic respiration. In green sulphur bacteria and heliobacteria, menaquinones are thought to be used as a loosely bound secondary electron acceptor in the photosynthetic reaction centre. In cyanobacteria, the product of the menaquinone pathway is phylloquinone (2-methyl-3-phytyl-1,4-naphthoquinone), a molecule used exclusively as an electron transfer cofactor in Photosystem (PS) I. .; GO: 0008756 o-succinylbenzoate-CoA ligase activity, 0009234 menaquinone biosynthetic process.
Probab=24.83  E-value=63  Score=14.92  Aligned_cols=32  Identities=19%  Similarity=0.217  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHCCCCCCCEEEEEEECCCCCCCC
Q ss_conf             99999999853985340699997078987321
Q gi|254780881|r   58 LRSNAQQIIQNIPTVKNAVVTLTENKNPPQQR   89 (101)
Q Consensus        58 l~~~i~~~l~~i~gv~~v~V~lt~~~~~~~~~   89 (101)
                      --.+||+.|.++|+|..+-|.-..+.+|++.+
T Consensus       403 yP~EIE~v~~s~p~v~~a~vvp~~D~~wG~vP  434 (490)
T TIGR01923       403 YPEEIEKVLYSHPGVQEAVVVPKPDAEWGQVP  434 (490)
T ss_pred             CHHHHHHHHHCCCCEEEEEEECCCCCCCCCCC
T ss_conf             87999999853876268888478470017865


No 42 
>PRK06156 hypothetical protein; Provisional
Probab=24.62  E-value=63  Score=14.90  Aligned_cols=59  Identities=2%  Similarity=-0.006  Sum_probs=38.4

Q ss_pred             CCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             87999762323870101336987999999672222068999999999985398534069999
Q gi|254780881|r   18 IPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL   79 (101)
Q Consensus        18 dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l   79 (101)
                      |..+|.--+..|.+   ..+++...+.+.+-+|-....+.+..++.+++.....-..+.+.+
T Consensus       369 De~sG~LT~n~gii---~~~~~~~~l~iniRyPv~~~~e~l~~~i~~~l~~~~~~~~~~l~i  427 (522)
T PRK06156        369 DDFMGPLTLSPTVV---KQTDKGTEVTVNLRRPVGKTPELLKGEIAEALAKWQAKHQVTLDI  427 (522)
T ss_pred             CCCCCCCEEEEEEE---EEECCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             68876847986899---997988999999968898888999999999999878752836987


No 43 
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme  (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.62  E-value=63  Score=14.90  Aligned_cols=51  Identities=16%  Similarity=0.154  Sum_probs=33.7

Q ss_pred             CCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf             9997623238701013369879999996722220689999999999853985340699
Q gi|254780881|r   20 GEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVV   77 (101)
Q Consensus        20 ~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V   77 (101)
                      +.|-||.+...++.   ..+....+++...+...    ..+.+-++|+++||++-.+|
T Consensus        22 ~~GGnI~~idvve~---~~~~~v~Ditv~~~d~~----h~~~Iv~al~~l~gV~V~~v   72 (74)
T cd04887          22 EAGGDIGAIDLVEQ---GRDYTVRDITVDAPSEE----HAETIVAAVRALPEVKVLSV   72 (74)
T ss_pred             HCCCCEEEEEEEEE---CCCEEEEEEEEECCCHH----HHHHHHHHHHCCCCEEEEEE
T ss_conf             76985677899994---49959999999869778----89999999961998599994


No 44 
>pfam02391 MoaE MoaE protein. This family contains the MoaE protein that is involved in biosynthesis of molybdopterin. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.
Probab=24.59  E-value=63  Score=14.89  Aligned_cols=68  Identities=7%  Similarity=0.029  Sum_probs=44.2

Q ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf             99999841418799976232387010133698799999967222206899999999998539853406999
Q gi|254780881|r    8 QIVDSLKVLSIPGEKNNIVEMQRLSEIFIVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVT   78 (101)
Q Consensus         8 ~I~~~L~~v~dP~~~~~iv~~g~V~~i~i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~   78 (101)
                      ++...++.+.+|..|--..-.|.|++-.  +|.-.-.|++..........++.-++++..+.+ +..+.+.
T Consensus        10 d~~~~~~~~~~~~~GAiv~F~G~VR~~~--~g~~v~~L~ye~y~~mA~~~l~~I~~~a~~k~~-~~~v~i~   77 (117)
T pfam02391        10 DVDEVIEKVSEPSAGAIVTFVGTVRDHN--GGKRVSRLEYEAYPEMAEKELAEIVEEAREKWP-GIDVAVV   77 (117)
T ss_pred             CHHHHHHHHCCCCCCEEEEEEEEECCCC--CCCCEEEEEEEECHHHHHHHHHHHHHHHHHHCC-CCCEEEE
T ss_conf             9899999821999988999999978899--998478999998228999999999999997579-8655899


No 45 
>TIGR02347 chap_CCT_zeta T-complex protein 1, zeta subunit; InterPro: IPR012722    Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT zeta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=23.61  E-value=66  Score=14.78  Aligned_cols=57  Identities=9%  Similarity=0.066  Sum_probs=43.6

Q ss_pred             HHHCCCCCCC-CCHHHCCCCCCCCCCCCEEE----------EEEEECHHHCHHHHHHHHHHHHHHHCCC
Q ss_conf             8414187999-76232387010133698799----------9999672222068999999999985398
Q gi|254780881|r   13 LKVLSIPGEK-NNIVEMQRLSEIFIVHNTVY----------LSITVPHTIAHQLQSLRSNAQQIIQNIP   70 (101)
Q Consensus        13 L~~v~dP~~~-~~iv~~g~V~~i~i~~~~v~----------i~l~l~~~~~~~~~~l~~~i~~~l~~i~   70 (101)
                      +-.|.| ... .++==+|+||+..+.+.+=+          ++|-+-.|......|+++.+++-|+++.
T Consensus       342 ~NSv~d-L~Pfe~LG~AGlVYE~~~GEEKyTFiEe~~~PkScTiLIkGpn~~ti~QiKDAvRDGLRAv~  409 (548)
T TIGR02347       342 LNSVED-LTPFECLGWAGLVYETVIGEEKYTFIEEVKNPKSCTILIKGPNDHTIKQIKDAVRDGLRAVK  409 (548)
T ss_pred             CCCCCC-CCCHHHCCCCCEEEEEEECCCCCEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHH
T ss_conf             374246-87311237652134135568500022103878616887328864467764676652257645


No 46 
>pfam09580 Spore_YhcN_YlaJ Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ). This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=23.50  E-value=67  Score=14.77  Aligned_cols=42  Identities=7%  Similarity=0.296  Sum_probs=20.6

Q ss_pred             CCCCEEEEEEEECHHHCHHHHHHHHHHHHHHHCC-CCCCCEEE
Q ss_conf             3698799999967222206899999999998539-85340699
Q gi|254780881|r   36 IVHNTVYLSITVPHTIAHQLQSLRSNAQQIIQNI-PTVKNAVV   77 (101)
Q Consensus        36 i~~~~v~i~l~l~~~~~~~~~~l~~~i~~~l~~i-~gv~~v~V   77 (101)
                      +.|..+.|.+.+........+.++++++++++.. |.+..|-|
T Consensus        88 Vt~~~a~V~v~~~~~~~~~~~~ik~~V~~~v~~~~p~~~~VyV  130 (169)
T pfam09580        88 VTGEEALVAVDLDNGERSLTEEIKKQVKKAVKSVDPRIYNVYV  130 (169)
T ss_pred             EECCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             9899799999738864035899999999999840888656999


No 47 
>pfam00873 ACR_tran AcrB/AcrD/AcrF family. Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer membrane channel TolC. The structure shows the AcrB forms a homotrimer.
Probab=22.79  E-value=69  Score=14.69  Aligned_cols=35  Identities=11%  Similarity=0.174  Sum_probs=15.0

Q ss_pred             EEEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             99999672222068999999999985398534069
Q gi|254780881|r   42 YLSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAV   76 (101)
Q Consensus        42 ~i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~   76 (101)
                      .+.+.+..+.......+.+++++.|+++||+.+++
T Consensus       672 ~i~i~l~G~d~~~L~~~a~~v~~~L~~~~gv~~v~  706 (1021)
T pfam00873       672 DLQVKIFGDGLDALDEARNQILAALAQLPGLADVR  706 (1021)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             79999479999999999999999983599817875


No 48 
>KOG4656 consensus
Probab=22.43  E-value=70  Score=14.65  Aligned_cols=25  Identities=16%  Similarity=0.347  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             9999999999853985340699997
Q gi|254780881|r   56 QSLRSNAQQIIQNIPTVKNAVVTLT   80 (101)
Q Consensus        56 ~~l~~~i~~~l~~i~gv~~v~V~lt   80 (101)
                      +.-..+++..|+.++||++|+|.+.
T Consensus        18 escvnavk~~L~~V~Gi~~vevdle   42 (247)
T KOG4656          18 ESCVNAVKACLKGVPGINSVEVDLE   42 (247)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEEEHH
T ss_conf             7788999998606887104787710


No 49 
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=21.36  E-value=74  Score=14.52  Aligned_cols=19  Identities=26%  Similarity=0.256  Sum_probs=8.8

Q ss_pred             HHHHHHHHHCCCCCCCEEE
Q ss_conf             9999999853985340699
Q gi|254780881|r   59 RSNAQQIIQNIPTVKNAVV   77 (101)
Q Consensus        59 ~~~i~~~l~~i~gv~~v~V   77 (101)
                      ...++..|+.+|||.+|.+
T Consensus       159 ~~~l~~~L~~i~GV~~V~~  177 (1025)
T PRK10614        159 STQLAQTIAQIDGVGDVDV  177 (1025)
T ss_pred             HHHHHHHHHCCCCCEEEEE
T ss_conf             9999999857989269997


No 50 
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=21.14  E-value=53  Score=15.34  Aligned_cols=42  Identities=17%  Similarity=0.256  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHHHHCC---CCCCCCCHHHCCCCCCCCCCCCEEEEEE
Q ss_conf             6035899999984141---8799976232387010133698799999
Q gi|254780881|r    2 NQILKNQIVDSLKVLS---IPGEKNNIVEMQRLSEIFIVHNTVYLSI   45 (101)
Q Consensus         2 s~~~~~~I~~~L~~v~---dP~~~~~iv~~g~V~~i~i~~~~v~i~l   45 (101)
                      .|+|+.+|++||++.+   .=++..|+|.+..|+.|  .|==|.|.|
T Consensus       840 HEVT~rAi~eAl~s~rkGeel~vd~NLVkAQvVRRI--~DRWiGF~L  884 (1843)
T TIGR01054       840 HEVTKRAILEALESPRKGEELSVDENLVKAQVVRRI--EDRWIGFTL  884 (1843)
T ss_pred             CCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEE--EEEEECEEE
T ss_conf             562379999986087657501000231011588898--754003011


No 51 
>PRK13614 lipoprotein LpqB; Provisional
Probab=21.05  E-value=75  Score=14.48  Aligned_cols=48  Identities=17%  Similarity=0.252  Sum_probs=37.8

Q ss_pred             CCCCCCCCEEEEEEEEC---HHHCHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             10133698799999967---2222068999999999985398534069999
Q gi|254780881|r   32 SEIFIVHNTVYLSITVP---HTIAHQLQSLRSNAQQIIQNIPTVKNAVVTL   79 (101)
Q Consensus        32 ~~i~i~~~~v~i~l~l~---~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~l   79 (101)
                      ..+.+.+|..++.|..+   .........|..++...|.+++++.+|++..
T Consensus       238 ~~V~v~~g~a~VdLs~~~~~~a~~~~r~~maaQL~~TL~~lp~V~~V~L~~  288 (573)
T PRK13614        238 ESVPVVSGTATVDLSAKELDPASAEDRQRMQQQLQLTLRAQPDVENVELRA  288 (573)
T ss_pred             CCEEECCCEEEEECCHHCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEE
T ss_conf             745403884798524020465899999999999999985489612699998


No 52 
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=20.55  E-value=77  Score=14.42  Aligned_cols=36  Identities=11%  Similarity=0.174  Sum_probs=25.7

Q ss_pred             EEEEECHHHCHHHHHHHHHHHHHHHCCCCCCCEEEEEEE
Q ss_conf             999967222206899999999998539853406999970
Q gi|254780881|r   43 LSITVPHTIAHQLQSLRSNAQQIIQNIPTVKNAVVTLTE   81 (101)
Q Consensus        43 i~l~l~~~~~~~~~~l~~~i~~~l~~i~gv~~v~V~lt~   81 (101)
                      ..+.++.-.|   ..=...++++|+.++|+.++.|.+..
T Consensus         4 ~~l~v~~MtC---~~C~~~V~~al~~v~gv~~v~v~l~~   39 (71)
T COG2608           4 TTLKVEGMTC---GHCVKTVEKALEEVDGVASVDVDLEK   39 (71)
T ss_pred             EEEEECCCCC---HHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             6997779294---89999999988438982399995221


No 53 
>TIGR00855 L12 ribosomal protein L7/L12; InterPro: IPR000206   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   This family of large subunit ribosomal proteins is called the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain . The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=20.01  E-value=66  Score=14.79  Aligned_cols=18  Identities=39%  Similarity=0.717  Sum_probs=14.7

Q ss_pred             CCCCCHHHHHHHHHHCCC
Q ss_conf             960358999999841418
Q gi|254780881|r    1 MNQILKNQIVDSLKVLSI   18 (101)
Q Consensus         1 Ms~~~~~~I~~~L~~v~d   18 (101)
                      |+.++.++|++.|+..+-
T Consensus         1 Ma~l~~~~i~E~l~~~tv   18 (131)
T TIGR00855         1 MAKLSKEQIIEALKSLTV   18 (131)
T ss_pred             CCCCCHHHHHHHHHCCCH
T ss_conf             976658899999866803


Done!