Query         gi|254781064|ref|YP_003065477.1| FeS assembly scaffold SufA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 116
No_of_seqs    111 out of 2959
Neff          7.0 
Searched_HMMs 39220
Date          Mon May 30 05:14:15 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781064.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00049 TIGR00049 iron-sulfu 100.0 1.1E-43       0  266.2   9.9  104    5-111     1-105 (105)
  2 PRK13623 iron-sulfur cluster i 100.0 3.7E-40 9.8E-45  246.4  12.3  110    1-111     9-118 (118)
  3 PRK09502 iscA iron-sulfur clus 100.0 6.2E-39 1.6E-43  239.5  11.8  106    4-111     2-107 (107)
  4 COG0316 sufA Fe-S cluster asse 100.0 8.5E-39 2.2E-43  238.7  11.8  110    1-111     1-110 (110)
  5 PRK09504 sufA iron-sulfur clus 100.0 4.4E-38 1.1E-42  234.7  11.5  107    3-111    16-122 (122)
  6 TIGR01997 sufA_proteo FeS asse 100.0 7.7E-37   2E-41  227.7   9.7  108    3-111     1-110 (110)
  7 KOG1120 consensus              100.0   6E-34 1.5E-38  211.5   7.7  108    2-111    27-134 (134)
  8 PRK11190 putative DNA uptake p 100.0 1.3E-28 3.3E-33  181.5  10.7   99    4-103     1-100 (192)
  9 TIGR03341 YhgI_GntY IscR-regul 100.0 1.4E-28 3.6E-33  181.3  10.3   96    5-101     1-97  (190)
 10 TIGR02011 IscA iron-sulfur clu 100.0 4.3E-29 1.1E-33  184.2   7.3  105    5-111     1-105 (105)
 11 KOG1119 consensus              100.0 7.7E-29   2E-33  182.8   7.5  106    3-112    92-198 (199)
 12 pfam01521 Fe-S_biosyn Iron-sul  99.9 2.1E-27 5.3E-32  174.8  10.4   91    5-97      1-91  (91)
 13 TIGR01911 HesB_rel_seleno HesB  98.9   1E-08 2.6E-13   69.9   8.5   89    4-94      3-92  (93)
 14 COG4841 Uncharacterized protei  98.1 4.6E-06 1.2E-10   55.0   5.4   88    5-94      3-94  (95)
 15 COG4918 Uncharacterized protei  97.2 0.00066 1.7E-08   42.9   5.3   78    5-85      3-84  (114)
 16 COG3564 Uncharacterized protei  95.3    0.15 3.8E-06   29.7   8.0   94    1-100     3-101 (116)
 17 pfam05610 DUF779 Protein of un  93.9    0.34 8.7E-06   27.7   7.1   79   15-99      3-86  (95)
 18 KOG4777 consensus               75.7     2.1 5.2E-05   23.3   2.2   44   61-105   114-157 (361)
 19 TIGR02176 pyruv_ox_red pyruvat  53.1      21 0.00054   17.6   4.2   56    8-68    945-1013(1194)
 20 COG4647 AcxC Acetone carboxyla  52.1     6.6 0.00017   20.5   1.1   33   79-111    44-81  (165)
 21 cd01531 Acr2p Eukaryotic arsen  51.1      14 0.00035   18.7   2.6   20   13-34      7-26  (113)
 22 TIGR01369 CPSaseII_lrg carbamo  46.5     8.9 0.00023   19.8   1.0   46    6-62    254-300 (1089)
 23 TIGR01074 rep ATP-dependent DN  41.2      30 0.00077   16.8   3.1   68    5-81     54-123 (677)
 24 COG4393 Predicted membrane pro  37.3      38 0.00096   16.2   3.1   13    6-18    228-240 (405)
 25 KOG0259 consensus               37.1      39 0.00098   16.2   3.6   73   34-112   131-219 (447)
 26 PRK03824 hypA hydrogenase nick  32.9      24 0.00061   17.4   1.5   35    5-40      4-38  (135)
 27 COG0686 Ald Alanine dehydrogen  32.3      46  0.0012   15.7   3.0   69   16-91    252-328 (371)
 28 TIGR02588 TIGR02588 conserved   32.0      42  0.0011   16.0   2.6   67   30-100    35-110 (122)
 29 KOG3348 consensus               30.8      49  0.0013   15.6   4.0   37   11-49      4-40  (85)
 30 TIGR00636 PduO_Nterm ATP:cob(I  30.6      26 0.00067   17.1   1.4   36    3-38     84-119 (184)
 31 PRK13696 hypothetical protein;  27.0      51  0.0013   15.5   2.3   19    1-19      2-20  (72)
 32 pfam01155 HypA Hydrogenase exp  26.6      39 0.00099   16.2   1.7   35    5-40      3-37  (112)
 33 TIGR01323 nitrile_alph nitrile  26.6      59  0.0015   15.2   3.2   29    7-35     16-44  (186)
 34 cd03377 TPP_PFOR_PNO Thiamine   25.2      58  0.0015   15.2   2.3   28   39-71    160-189 (365)
 35 KOG3580 consensus               24.1      31  0.0008   16.7   0.8   54   52-112   447-508 (1027)
 36 PRK00564 hypA hydrogenase nick  23.8      39   0.001   16.1   1.3   35    5-40      4-38  (117)
 37 TIGR01265 tyr_nico_aTase tyros  22.0      62  0.0016   15.0   2.0   98    9-112    83-204 (424)
 38 pfam12141 DUF3589 Protein of u  21.6      33 0.00085   16.5   0.5   20   91-110   337-357 (488)
 39 KOG0387 consensus               21.2      46  0.0012   15.8   1.2   98    4-106   258-361 (923)
 40 TIGR02168 SMC_prok_B chromosom  21.1      61  0.0016   15.1   1.8   18    4-21    555-572 (1191)
 41 cd01234 PH_CADPS CADPS (Ca2+-d  20.1      68  0.0017   14.8   1.9   31   69-99     45-85  (117)

No 1  
>TIGR00049 TIGR00049 iron-sulfur cluster assembly accessory protein; InterPro: IPR016092   This family includes HesB which may be involved in nitrogen fixation; the hesB gene is expressed only under nitrogen fixation conditions . Other members of this family include various hypothetical proteins that also contain the NifU-like domain (IPR001075 from INTERPRO). NifU-like proteins are found in species as divergent as humans and H. influenzae suggesting that these proteins perform some basic cellular function .; GO: 0005198 structural molecule activity, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly.
Probab=100.00  E-value=1.1e-43  Score=266.17  Aligned_cols=104  Identities=43%  Similarity=0.832  Sum_probs=98.8

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCC-CCCEECCCCEEEEECHHHHHHHCCCEEEE
Q ss_conf             65268999999999971799861899998479878711320011002101-22201246839999787732006989976
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVD-GDDLIEKDGVKVWIDSASLLYMLGTEIDF   83 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~-~D~~~~~~g~~i~id~~s~~~L~g~~IDy   83 (116)
                      |+|||+|++||+.++++++.  .+|||.|++||||||+|.|+|+ +++.+ +|.+++.+|++|+||++|++||.|++|||
T Consensus         1 i~LTd~A~~~~~~l~~~~~~--~~LRv~V~~GGCSG~~Y~l~~~-~~~~~~dD~v~~~~Gv~v~vD~~S~~~l~G~~~Dy   77 (105)
T TIGR00049         1 ITLTDSAAKRIKALLAGEGE--LGLRVGVKGGGCSGLQYGLEFD-DEPNEKDDEVFEQDGVKVVVDPKSLPYLNGSEIDY   77 (105)
T ss_pred             CEECHHHHHHHHHHHHHCCC--CEEEEEEECCCCCCEEEEEECC-CCCCCCCCEEEEECCEEEEECCCCHHHHCCCEEEE
T ss_conf             90188999999999871589--3278986077757602310011-48899988788638828988154145425877778


Q ss_pred             ECCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             3177445128988887876788521121
Q gi|254781064|r   84 KTEKLYSGFVFHNPNQVSACGCGQSVEI  111 (116)
Q Consensus        84 ~~~~~~~~F~~~NPna~~~CgCG~SF~~  111 (116)
                      ++++++++|+|+||||+++||||+||++
T Consensus        78 v~~l~~sgF~f~NPNA~~~CGCG~SF~~  105 (105)
T TIGR00049        78 VEELEGSGFTFTNPNAKGTCGCGKSFSV  105 (105)
T ss_pred             EECCCCCCCEEECCCCCCCCCCCCCCCC
T ss_conf             7356778337764864674787776889


No 2  
>PRK13623 iron-sulfur cluster insertion protein ErpA; Provisional
Probab=100.00  E-value=3.7e-40  Score=246.35  Aligned_cols=110  Identities=33%  Similarity=0.621  Sum_probs=104.1

Q ss_pred             CCCCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCE
Q ss_conf             98616526899999999997179986189999847987871132001100210122201246839999787732006989
Q gi|254781064|r    1 MSDIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTE   80 (116)
Q Consensus         1 M~~mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~   80 (116)
                      |+..|+||++|++||++++++++.+..+|||+|++|||+||+|.|.+. +.+.++|.+++.+|++|+||+.|++||+|++
T Consensus         9 ~p~~ItiT~~A~~~ik~ll~~~~~~~~~lRv~V~~gGCsG~~Y~~~~~-~~~~~dD~v~~~~g~~v~Id~~Sl~~L~Gs~   87 (118)
T PRK13623          9 VPLPLVFTDAAAAKVKELIEEEGNPDLKLRVYITGGGCSGFQYGFTFD-EQVNEDDTTIEKQGVTLVVDPMSLQYLVGAE   87 (118)
T ss_pred             CCCCCEECHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCEEEEEEEC-CCCCCCCCEEEECCEEEEECHHHHHHCCCCE
T ss_conf             998749999999999999986899961799999578789828567987-5568888679837869999988984528989


Q ss_pred             EEEECCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             9763177445128988887876788521121
Q gi|254781064|r   81 IDFKTEKLYSGFVFHNPNQVSACGCGQSVEI  111 (116)
Q Consensus        81 IDy~~~~~~~~F~~~NPna~~~CgCG~SF~~  111 (116)
                      |||++++++++|+|+||||+++||||+||++
T Consensus        88 IDy~e~~~gs~F~f~NPna~~~CGCG~SFsv  118 (118)
T PRK13623         88 VDYTEGLEGSRFVIKNPNAKTTCGCGSSFSI  118 (118)
T ss_pred             EEEEECCCCCCEEEECCCCCCCCCCCCCCCC
T ss_conf             9887669867169989898854699877349


No 3  
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=100.00  E-value=6.2e-39  Score=239.45  Aligned_cols=106  Identities=38%  Similarity=0.784  Sum_probs=99.5

Q ss_pred             CEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCEEEE
Q ss_conf             16526899999999997179986189999847987871132001100210122201246839999787732006989976
Q gi|254781064|r    4 IVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEIDF   83 (116)
Q Consensus         4 mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~IDy   83 (116)
                      .|+||++|+++|++++++++ +.++|||+|++|||+||+|.|++. +++.++|.+++.+|++|+||+.|++||.|++|||
T Consensus         2 ~I~iT~~A~~~i~~~l~~~~-~~~~lRl~Vk~gGCsG~~Y~l~~~-~~~~~~D~~~~~~g~~i~Id~~s~~~l~G~~IDy   79 (107)
T PRK09502          2 SITLSDSAAARVNTFLANRG-KGFGLRLGVRTSGCSGMAYVLEFV-DEPTPEDIVFEDKGVKVVVDGKSLQFLDGTQLDF   79 (107)
T ss_pred             EEEECHHHHHHHHHHHHHCC-CCEEEEEEEECCCCCCEEEEEEEC-CCCCCCCEEEEECCEEEEECHHHHHHHCCCEEEE
T ss_conf             79999999999999997479-970899999357758858375883-5578997999869989999879987757889977


Q ss_pred             ECCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             3177445128988887876788521121
Q gi|254781064|r   84 KTEKLYSGFVFHNPNQVSACGCGQSVEI  111 (116)
Q Consensus        84 ~~~~~~~~F~~~NPna~~~CgCG~SF~~  111 (116)
                      ++++++++|+|+||||+++||||+||++
T Consensus        80 ~~~~~~~gF~f~NPna~~~CGCG~SF~i  107 (107)
T PRK09502         80 VKEGLNEGFKFTNPNVKDECGCGESFHV  107 (107)
T ss_pred             EECCCCCCEEEECCCCCCCCCCCCCCCC
T ss_conf             3168846179989798850489877419


No 4  
>COG0316 sufA Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00  E-value=8.5e-39  Score=238.70  Aligned_cols=110  Identities=40%  Similarity=0.764  Sum_probs=104.9

Q ss_pred             CCCCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCE
Q ss_conf             98616526899999999997179986189999847987871132001100210122201246839999787732006989
Q gi|254781064|r    1 MSDIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTE   80 (116)
Q Consensus         1 M~~mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~   80 (116)
                      |..||+||++|++|++.++++++.++.+|||+|++|||+||+|.|+|++ .+.++|.+++.+|++|+||+.|++||.|++
T Consensus         1 ~~~~itlT~~Aa~~v~~ll~~~~~~~~~lRv~V~~gGCsG~~Y~~~~~~-~~~~~D~v~e~~g~~v~vD~~S~~~L~G~~   79 (110)
T COG0316           1 AAMMITLTDAAAARVKALLAKEGEENLGLRVGVKGGGCSGFQYGLEFDD-EINEDDTVFEQDGVKVVVDPKSLPYLEGTE   79 (110)
T ss_pred             CCCCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEEECC-CCCCCCEEEEECCEEEEECHHHHHHHCCCE
T ss_conf             9874044999999999999716588856899984897789376778866-789998799859989998752665646988


Q ss_pred             EEEECCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             9763177445128988887876788521121
Q gi|254781064|r   81 IDFKTEKLYSGFVFHNPNQVSACGCGQSVEI  111 (116)
Q Consensus        81 IDy~~~~~~~~F~~~NPna~~~CgCG~SF~~  111 (116)
                      |||+++.+|++|+|+||||+++||||+||++
T Consensus        80 IDyv~~~~g~~F~~~NPNA~~~CgCg~Sf~v  110 (110)
T COG0316          80 IDYVEDLLGSGFTFKNPNAKSSCGCGESFSV  110 (110)
T ss_pred             EEEEECCCCCCEEEECCCCCCCCCCCCCCCC
T ss_conf             8887747677348979998762028887779


No 5  
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=100.00  E-value=4.4e-38  Score=234.69  Aligned_cols=107  Identities=36%  Similarity=0.705  Sum_probs=98.6

Q ss_pred             CCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCEEE
Q ss_conf             61652689999999999717998618999984798787113200110021012220124683999978773200698997
Q gi|254781064|r    3 DIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEID   82 (116)
Q Consensus         3 ~mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~ID   82 (116)
                      +-|+||++|++||+++++++ ++..+|||+|++|||+||+|.|+|+. .+.++|.+++.+|++|+||++|++||+|++||
T Consensus        16 ~~ItiT~~A~~~i~~l~~~~-~~~~~lRl~Vk~gGCsG~~Y~~~~~~-~~~~~D~v~~~~g~~v~vd~~s~~~l~Gt~ID   93 (122)
T PRK09504         16 QGLTLTPAAAAHIRELMAKQ-PGMKGVRLGVKQTGCAGFGYVLDSVS-EPDKDDLVFEHDGAKLFVPLQAMPFIDGTEVD   93 (122)
T ss_pred             CCEEECHHHHHHHHHHHHHC-CCCCEEEEEEECCCCCCEEEEEEECC-CCCCCCEEEEECCEEEEECHHHHCCCCCCEEE
T ss_conf             44899999999999999749-99727999993877588898706437-89999999983997999874783732798998


Q ss_pred             EECCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             63177445128988887876788521121
Q gi|254781064|r   83 FKTEKLYSGFVFHNPNQVSACGCGQSVEI  111 (116)
Q Consensus        83 y~~~~~~~~F~~~NPna~~~CgCG~SF~~  111 (116)
                      |++++++++|+|+||||+++||||+||++
T Consensus        94 y~~~~~~~~F~f~NPna~~~CGCG~SF~V  122 (122)
T PRK09504         94 YVREGLNQIFKFHNPKAQNECGCGESFGV  122 (122)
T ss_pred             EEECCCCCCEEEECCCCCCCCCCCCCCCC
T ss_conf             86768867369989898851489877249


No 6  
>TIGR01997 sufA_proteo FeS assembly scaffold SufA; InterPro: IPR011298   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents the SufA protein of the SUF system of iron-sulphur cluster biosynthesis. SufA acts as a scaffold in which Fe and S are assembled into FeS clusters . This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria..
Probab=100.00  E-value=7.7e-37  Score=227.71  Aligned_cols=108  Identities=49%  Similarity=0.942  Sum_probs=102.0

Q ss_pred             CCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEEC-CCCEEEEECHHHHHHHCCCEE
Q ss_conf             6165268999999999971799861899998479878711320011002101222012-468399997877320069899
Q gi|254781064|r    3 DIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIE-KDGVKVWIDSASLLYMLGTEI   81 (116)
Q Consensus         3 ~mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~-~~g~~i~id~~s~~~L~g~~I   81 (116)
                      .+|++|++|+.||++|+++++.+..++||+||.+||+||.|.++++.+ |.++|.+++ .+|.+|+|+|++++||+||.+
T Consensus         1 ~~~~lT~AAa~~i~~l~~~~g~~~~g~Rl~vKktGCaG~~Y~~~~V~e-p~~~D~L~et~~Gakv~v~p~a~~~i~GT~v   79 (110)
T TIGR01997         1 AVITLTDAAATHIRELVKKRGTEAVGIRLSVKKTGCAGMEYVLELVSE-PKEDDDLIETADGAKVFVAPEAVLFILGTQV   79 (110)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCEEEEEEECC-CCCCCEEEECCCCCEEEECHHHHHHCCCCEE
T ss_conf             965201578899999985038982048876655763773023001107-8888703210388658866444002048674


Q ss_pred             EEECCCCCC-EEEEECCCCCCCCCCCCCCCC
Q ss_conf             763177445-128988887876788521121
Q gi|254781064|r   82 DFKTEKLYS-GFVFHNPNQVSACGCGQSVEI  111 (116)
Q Consensus        82 Dy~~~~~~~-~F~~~NPna~~~CgCG~SF~~  111 (116)
                      ||+...+++ +|.|+|||+++.|||||||++
T Consensus        80 Df~~~~L~~y~f~FnNPn~~~aCGCGES~~l  110 (110)
T TIGR01997        80 DFVKTTLRQYGFKFNNPNATSACGCGESFEL  110 (110)
T ss_pred             EEEECCCCEEEEEECCCCCCCCCCCCCCCCC
T ss_conf             5787354122227428554678876421459


No 7  
>KOG1120 consensus
Probab=100.00  E-value=6e-34  Score=211.49  Aligned_cols=108  Identities=37%  Similarity=0.751  Sum_probs=100.9

Q ss_pred             CCCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCEE
Q ss_conf             86165268999999999971799861899998479878711320011002101222012468399997877320069899
Q gi|254781064|r    2 SDIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEI   81 (116)
Q Consensus         2 ~~mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~I   81 (116)
                      ++.|++||.|.+||++++++ .++...|||+|+.+||||++|.+++. +.+.+.|++++++|++|+|+|+++..|.|+++
T Consensus        27 k~~ltLTp~Av~~ik~ll~~-~~e~~~lrigVk~rGCnGlsYtleY~-~~kgkfDE~VeqdGv~I~ie~KA~l~liGteM  104 (134)
T KOG1120          27 KAALTLTPSAVNHIKQLLSD-KPEDVCLRIGVKQRGCNGLSYTLEYT-KTKGKFDEVVEQDGVRIFIEPKALLTLIGTEM  104 (134)
T ss_pred             CCCCCCCHHHHHHHHHHHHH-CCCCCEEEEEEECCCCCCCEEEEEEE-CCCCCCCCEEEECCCEEEECCCCEEEECCCEE
T ss_conf             56120598999999999974-87676168877517757635552200-16898755145447089981401046612110


Q ss_pred             EEECCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             763177445128988887876788521121
Q gi|254781064|r   82 DFKTEKLYSGFVFHNPNQVSACGCGQSVEI  111 (116)
Q Consensus        82 Dy~~~~~~~~F~~~NPna~~~CgCG~SF~~  111 (116)
                      ||+++.++++|+|.|||++++||||+||++
T Consensus       105 DyvddkL~Sefvf~npna~gtcGcgeSf~~  134 (134)
T KOG1120         105 DYVDDKLSSEFVFSNPNAKGTCGCGESFSV  134 (134)
T ss_pred             HHHHHHHCCCEEEECCCCCCCCCCCCCCCC
T ss_conf             144565317357617886653246633459


No 8  
>PRK11190 putative DNA uptake protein; Provisional
Probab=99.96  E-value=1.3e-28  Score=181.53  Aligned_cols=99  Identities=23%  Similarity=0.355  Sum_probs=91.0

Q ss_pred             CEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHH-HCCCCCCCCEECCCCEEEEECHHHHHHHCCCEEE
Q ss_conf             165268999999999971799861899998479878711320011-0021012220124683999978773200698997
Q gi|254781064|r    4 IVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLV-TDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEID   82 (116)
Q Consensus         4 mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~-~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~ID   82 (116)
                      ||+||++|+++|++++++++ ++.+|||.|+++||+||+|.|.|. .+...++|.+++.+|++|+||+.|++||+|++||
T Consensus         1 MItITd~A~~~l~~LL~~q~-~g~~LRV~V~~~Gcsgaey~~~f~~~de~~~dD~~~e~~gf~V~VD~~S~~yL~ga~ID   79 (192)
T PRK11190          1 MITISDAAQAHFAKLLANQE-EGTQIRVFVINPGTPNAECGVSYCPPDAVEATDTELKFNGFSAYVDELSAPFLEDAEID   79 (192)
T ss_pred             CEEECHHHHHHHHHHHHCCC-CCCEEEEEEECCCCCCCEEEEEECCCCCCCCCEEEEEECCEEEEECCCHHHHHCCCEEE
T ss_conf             95868999999999984388-89639999945998995688897467778885289986999999830266786788997


Q ss_pred             EECCCCCCEEEEECCCCCCCC
Q ss_conf             631774451289888878767
Q gi|254781064|r   83 FKTEKLYSGFVFHNPNQVSAC  103 (116)
Q Consensus        83 y~~~~~~~~F~~~NPna~~~C  103 (116)
                      |+++.+|++|+|+||||+...
T Consensus        80 y~~d~~G~~ftIkNPNAK~~~  100 (192)
T PRK11190         80 FVTDQLGSQLTLKAPNAKMRK  100 (192)
T ss_pred             EECCCCCCEEEEECCCCCCCC
T ss_conf             652677877999899765555


No 9  
>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=99.96  E-value=1.4e-28  Score=181.35  Aligned_cols=96  Identities=24%  Similarity=0.364  Sum_probs=89.2

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHH-CCCCCCCCEECCCCEEEEECHHHHHHHCCCEEEE
Q ss_conf             652689999999999717998618999984798787113200110-0210122201246839999787732006989976
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVT-DNPVDGDDLIEKDGVKVWIDSASLLYMLGTEIDF   83 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~-~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~IDy   83 (116)
                      |+||++|+++|++++++++ ++.+|||+|+++||+||+|.|+|.. +...++|.+++.+|++|+||+.|++||+|++|||
T Consensus         1 ItITe~A~~~l~~Ll~~q~-~g~~lRv~V~~~Gcsg~qy~l~f~~~de~~~dD~~~e~~g~~V~VD~~S~~yL~Ga~IDy   79 (190)
T TIGR03341         1 ITITEAAQAYLAKLLAKQN-EGTGIRVFVVNPGTPYAECCVSYCPPDEVEPSDIKLEFNGFSAYVDALSAPFLEDAVIDF   79 (190)
T ss_pred             CEECHHHHHHHHHHHHCCC-CCCEEEEEEECCCCCCCEEEEEECCCCCCCCCCEEEEECCEEEEECCCHHHHHCCCEEEE
T ss_conf             9778999999999984088-895689999559999858887888877789987899849989998425467867889976


Q ss_pred             ECCCCCCEEEEECCCCCC
Q ss_conf             317744512898888787
Q gi|254781064|r   84 KTEKLYSGFVFHNPNQVS  101 (116)
Q Consensus        84 ~~~~~~~~F~~~NPna~~  101 (116)
                      +++.+|++|+|+||||+.
T Consensus        80 ~~d~~g~gfti~NPNAK~   97 (190)
T TIGR03341        80 VTDRMGGQLTLKAPNAKM   97 (190)
T ss_pred             ECCCCCCEEEEECCCCCC
T ss_conf             336768728997999765


No 10 
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA; InterPro: IPR011302   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents the IscA component of the ISC system for iron-sulphur cluster assembly. IscA is believed to act as a scaffold upon which 2Fe-2S clusters are assembled and subsequently transferred to ferredoxin , , . This clade is limited to the proteobacteria.; GO: 0005506 iron ion binding, 0005515 protein binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly.
Probab=99.96  E-value=4.3e-29  Score=184.25  Aligned_cols=105  Identities=42%  Similarity=0.809  Sum_probs=98.9

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCEEEEE
Q ss_conf             65268999999999971799861899998479878711320011002101222012468399997877320069899763
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEIDFK   84 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~IDy~   84 (116)
                      |++|++|.+++...+++.+ ++.+||++|+.+||+|+.|.++|++ ...++|.+++.+|++|+||++|+.||+|+.+||+
T Consensus         1 itl~~~a~~~~~~~la~rG-kG~G~rlG~~tsGCsGmay~lefvd-~~~~~d~~~~~~G~~~~~d~ksl~yl~G~~~d~~   78 (105)
T TIGR02011         1 ITLTEAAAERVNSFLANRG-KGLGLRLGVKTSGCSGMAYVLEFVD-EADDDDLVFEDKGVKIVIDAKSLVYLDGTQLDFV   78 (105)
T ss_pred             CCCCHHHHHHHHHHHHHCC-CCEEEEEEEEECCCCCEEEEEEECC-CCCCCCEEECCCCCEEEECCCEEEEECCCEEEEE
T ss_conf             9436778999999886148-8204674100036552000121102-6888853661687178981741343226222101


Q ss_pred             CCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             177445128988887876788521121
Q gi|254781064|r   85 TEKLYSGFVFHNPNQVSACGCGQSVEI  111 (116)
Q Consensus        85 ~~~~~~~F~~~NPna~~~CgCG~SF~~  111 (116)
                      .++++++|.|+|||++..||||+||++
T Consensus        79 keGl~eGf~f~nPn~k~~CGCGesf~v  105 (105)
T TIGR02011        79 KEGLNEGFKFENPNVKDECGCGESFHV  105 (105)
T ss_pred             ECHHHCCCEECCCCCCCCCCCCCCCCC
T ss_conf             001113731048876666677632349


No 11 
>KOG1119 consensus
Probab=99.95  E-value=7.7e-29  Score=182.82  Aligned_cols=106  Identities=29%  Similarity=0.603  Sum_probs=95.2

Q ss_pred             CCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCEEE
Q ss_conf             61652689999999999717998618999984798787113200110021012220124683999978773200698997
Q gi|254781064|r    3 DIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEID   82 (116)
Q Consensus         3 ~mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~ID   82 (116)
                      ..+.+++.|.++++++...  .+ ..||+.|++|||+||+|.|.+ +....++|.++..+|.+|+||..|+.+|+|+|||
T Consensus        92 ~~~~lsds~~krl~EI~~~--~p-e~LRl~VegGGCsGFQYkf~L-D~~in~dD~vf~e~~arVVvD~~SL~~~kGatvd  167 (199)
T KOG1119          92 FNLHLSDSCSKRLKEIYEN--SP-EFLRLTVEGGGCSGFQYKFRL-DNKINNDDRVFVENGARVVVDNVSLNLLKGATVD  167 (199)
T ss_pred             CEEEEHHHHHHHHHHHHHC--CC-CEEEEEEECCCCCCEEEEEEE-CCCCCCCCEEEEECCCEEEEECCCHHHCCCCEEE
T ss_conf             0488426778999999809--83-038999854870335888884-4777876657861880899853542112686333


Q ss_pred             EECCCCCCEEEE-ECCCCCCCCCCCCCCCCC
Q ss_conf             631774451289-888878767885211212
Q gi|254781064|r   83 FKTEKLYSGFVF-HNPNQVSACGCGQSVEIK  112 (116)
Q Consensus        83 y~~~~~~~~F~~-~NPna~~~CgCG~SF~~~  112 (116)
                      |.++++++.|.+ +||.|++.||||.||++|
T Consensus       168 y~~ELIrSsF~ivnNP~A~~gCsCgSSF~ik  198 (199)
T KOG1119         168 YTNELIRSSFRIVNNPSAKQGCSCGSSFDIK  198 (199)
T ss_pred             HHHHHHHHHHEEECCCCCCCCCCCCCCCCCC
T ss_conf             1788864110664283002587787654447


No 12 
>pfam01521 Fe-S_biosyn Iron-sulphur cluster biosynthesis. This family is involved in iron-sulphur cluster biosynthesis. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins.
Probab=99.95  E-value=2.1e-27  Score=174.82  Aligned_cols=91  Identities=45%  Similarity=0.779  Sum_probs=84.7

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCEEEEE
Q ss_conf             65268999999999971799861899998479878711320011002101222012468399997877320069899763
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEIDFK   84 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~IDy~   84 (116)
                      |+||++|+++|+++++.++. ..+|||+|++|||+||+|.|++. +++.++|.+++.+|++|+||+.|++||.|++|||+
T Consensus         1 ItiT~~A~~~i~~~l~~~~~-~~~lRl~v~~gGC~G~~Y~l~~~-~~~~~~D~~~~~~g~~v~Id~~s~~~l~g~~iDy~   78 (91)
T pfam01521         1 ITLTDAAAKWIKKLLDLEGG-ENGLRIGVRYGGCSGFSYGLTFE-DEAGEGDEVFEQDGVTVVVDEKSLPYLEGTEIDFV   78 (91)
T ss_pred             CEECHHHHHHHHHHHHHCCC-CCEEEEEEECCCCCCCEEEEEEC-CCCCCCCEEEEECCCEEEEEHHHHHHCCCCEEEEE
T ss_conf             99999999999999974899-94699999669979818878985-35777859999899299991699815599899986


Q ss_pred             CCCCCCEEEEECC
Q ss_conf             1774451289888
Q gi|254781064|r   85 TEKLYSGFVFHNP   97 (116)
Q Consensus        85 ~~~~~~~F~~~NP   97 (116)
                      +++++++|+|+||
T Consensus        79 ~~~~~~~F~f~NP   91 (91)
T pfam01521        79 EELLGSGFTFSNP   91 (91)
T ss_pred             ECCCCCEEEEECC
T ss_conf             2688773999595


No 13 
>TIGR01911 HesB_rel_seleno HesB-related (seleno)protein; InterPro: IPR010965   This entry represents a family of small proteins related to HesB and its close homologs, which are likely to be involved in iron-sulphur cluster assembly. Several members are selenoproteins, with a TGA codon and Sec residue that aligns to the conserved Cys of the HesB domain..
Probab=98.89  E-value=1e-08  Score=69.91  Aligned_cols=89  Identities=15%  Similarity=0.254  Sum_probs=78.8

Q ss_pred             CEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHH-HHCCCEEE
Q ss_conf             16526899999999997179986189999847987871132001100210122201246839999787732-00698997
Q gi|254781064|r    4 IVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLL-YMLGTEID   82 (116)
Q Consensus         4 mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~-~L~g~~ID   82 (116)
                      .++++|.|...+++.|++++.+.-.|||...|-||+|+.+.+..  +.+.++|.++...+++++||+.-.. ||....|.
T Consensus         3 kV~~SD~Ay~efldfLK~n~~d~~V~rI~f~G~g~~GP~F~~~i--~e~nenD~~~~i~d~~f~ID~~lid~flgef~I~   80 (93)
T TIGR01911         3 KVVMSDEAYKEFLDFLKKNDVDKDVVRIYFEGFGPSGPVFGIAI--AEKNENDEVVVIKDLTFLIDKSLIDQFLGEFSIS   80 (93)
T ss_pred             EEEECHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCEEEEEE--CCCCCCCEEEEECCEEEEECCHHHHHCCCEEEEE
T ss_conf             78851778888987620068987569995146258997557885--5879997478854427986502453308806998


Q ss_pred             EECCCCCCEEEE
Q ss_conf             631774451289
Q gi|254781064|r   83 FKTEKLYSGFVF   94 (116)
Q Consensus        83 y~~~~~~~~F~~   94 (116)
                      ..++-.+++|.+
T Consensus        81 ~~ee~fg~gl~l   92 (93)
T TIGR01911        81 LREENFGKGLKL   92 (93)
T ss_pred             EECCCCCCCEEE
T ss_conf             611337352030


No 14 
>COG4841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.13  E-value=4.6e-06  Score=55.01  Aligned_cols=88  Identities=20%  Similarity=0.383  Sum_probs=64.7

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEE--EHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCC--CE
Q ss_conf             6526899999999997179986189999847987871132--0011002101222012468399997877320069--89
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYM--VDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLG--TE   80 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~--l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g--~~   80 (116)
                      |+||+.|.+-+++-+.-.  ++-.+|+.|+-|||+-.+=.  +.+..+.|.+--..-+.+|++++|..+.+=|.++  .+
T Consensus         3 i~vtd~A~~wfk~E~~l~--~g~~vrffvRyGG~~~~~~GFS~gv~~e~PkE~g~~q~~Dgltffiee~DlWYF~d~d~~   80 (95)
T COG4841           3 IEVTDQALKWFKEELDLE--EGNKVRFFVRYGGCSSLQQGFSLGVAKEVPKEIGYKQEYDGLTFFIEEKDLWYFDDHDLK   80 (95)
T ss_pred             EEECHHHHHHHHHHCCCC--CCCEEEEEEEECCCCCCCCCCCEEEECCCCHHHCHHEEECCEEEEEECCCEEEECCCCEE
T ss_conf             587079888888743877--898789999976711236872313421283231522044570899945726887288679


Q ss_pred             EEEECCCCCCEEEE
Q ss_conf             97631774451289
Q gi|254781064|r   81 IDFKTEKLYSGFVF   94 (116)
Q Consensus        81 IDy~~~~~~~~F~~   94 (116)
                      |||..+-..-.|++
T Consensus        81 v~y~~~~Dei~fs~   94 (95)
T COG4841          81 VDYSPDTDEISFSY   94 (95)
T ss_pred             EECCCCCCCCEEEC
T ss_conf             96167877504631


No 15 
>COG4918 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=97.24  E-value=0.00066  Score=42.95  Aligned_cols=78  Identities=17%  Similarity=0.217  Sum_probs=58.5

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC---CEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHC-CCE
Q ss_conf             652689999999999717998618999984798787---1132001100210122201246839999787732006-989
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAG---LEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYML-GTE   80 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G---~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~-g~~   80 (116)
                      |++|++|+.+|++....+-....-+|+..++-+|+|   +.|.+.  .+. ...|..++.++..|+|-....-|+. ..+
T Consensus         3 Itftd~a~~~l~~a~d~nl~~~~hl~ydtEgc~Ca~SGi~t~rlv--ae~-tg~d~~idsn~gPiyik~~~~~Ff~D~mt   79 (114)
T COG4918           3 ITFTDKAADKLKAAGDVNLVFDDHLLYDTEGCACAGSGISTYRLV--AEE-TGFDASIDSNFGPIYIKDYGSYFFQDEMT   79 (114)
T ss_pred             EEECHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCEEEEE--EEC-CCCCCCCCCCCCCEEEEECCEEEECCEEE
T ss_conf             785289999999864368675415798054441026885349988--741-47430000478748997130067311323


Q ss_pred             EEEEC
Q ss_conf             97631
Q gi|254781064|r   81 IDFKT   85 (116)
Q Consensus        81 IDy~~   85 (116)
                      |||-+
T Consensus        80 idyN~   84 (114)
T COG4918          80 IDYNP   84 (114)
T ss_pred             EECCC
T ss_conf             42087


No 16 
>COG3564 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.27  E-value=0.15  Score=29.74  Aligned_cols=94  Identities=26%  Similarity=0.211  Sum_probs=62.7

Q ss_pred             CCCCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHC--CCCCCCCEE-CCCCEEEEECHHHHHHHC
Q ss_conf             98616526899999999997179986189999847987871132001100--210122201-246839999787732006
Q gi|254781064|r    1 MSDIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTD--NPVDGDDLI-EKDGVKVWIDSASLLYML   77 (116)
Q Consensus         1 M~~mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~--~~~~~D~~~-~~~g~~i~id~~s~~~L~   77 (116)
                      |..-++.|++|..-|.++.+++++    + +.-.+|||..-+--|-+...  -..++|..+ +.+|+.+||......+-+
T Consensus         3 ~~~~V~aT~aAl~Li~~l~~~hgp----v-mFHQSGGCCDGSsPMCYP~~~fivGd~DvlLG~i~gvPvyIs~~QyeaWK   77 (116)
T COG3564           3 MPARVLATPAALDLIAELQAEHGP----V-MFHQSGGCCDGSSPMCYPRADFIVGDNDVLLGEIDGVPVYISGPQYEAWK   77 (116)
T ss_pred             CCCCEECCHHHHHHHHHHHHHCCC----E-EEECCCCCCCCCCCCCCCCCCEEECCCCEEEEEECCEEEEECCCHHHHHH
T ss_conf             876224388899999999875498----7-88326884589987401454456647735886537877886470775210


Q ss_pred             CC--EEEEECCCCCCEEEEECCCCC
Q ss_conf             98--997631774451289888878
Q gi|254781064|r   78 GT--EIDFKTEKLYSGFVFHNPNQV  100 (116)
Q Consensus        78 g~--~IDy~~~~~~~~F~~~NPna~  100 (116)
                      .+  .||-+. +-|..|...|-.++
T Consensus        78 HTqLIIDVVp-GRGGmFSLdng~E~  101 (116)
T COG3564          78 HTQLIIDVVP-GRGGMFSLDNGREK  101 (116)
T ss_pred             CCEEEEEEEC-CCCCEEECCCCCCE
T ss_conf             0178999865-98864572578513


No 17 
>pfam05610 DUF779 Protein of unknown function (DUF779). This family consists of several bacterial proteins of unknown function.
Probab=93.86  E-value=0.34  Score=27.72  Aligned_cols=79  Identities=23%  Similarity=0.280  Sum_probs=52.2

Q ss_pred             HHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHC--CCCCCCCEE-CCCCEEEEECHHHHHHHCCC--EEEEECCCCC
Q ss_conf             999997179986189999847987871132001100--210122201-24683999978773200698--9976317744
Q gi|254781064|r   15 IKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTD--NPVDGDDLI-EKDGVKVWIDSASLLYMLGT--EIDFKTEKLY   89 (116)
Q Consensus        15 i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~--~~~~~D~~~-~~~g~~i~id~~s~~~L~g~--~IDy~~~~~~   89 (116)
                      |.++.++++ +   | +.-.+|||..=+--|-+...  ...+.|..+ +.+|+.+||++....|-+.|  +||-+. +.|
T Consensus         3 i~~L~~~HG-~---L-mFHQSGGCCDGSaPMC~p~gef~vg~~DV~LG~i~g~pfym~~~QfeyWkhT~l~iDvv~-GrG   76 (95)
T pfam05610         3 IRELKAKHG-P---L-MFHQSGGCCDGSAPMCYPKGEFIVGDSDVLLGEIGGVPFYISKSQFEYWKHTQLIIDVVP-GRG   76 (95)
T ss_pred             HHHHHHHHC-C---E-EEEECCCCCCCCCCCEECCCCCCCCCCCEEEEEECCEEEEECCHHHHHHHCCEEEEEEEC-CCC
T ss_conf             899987618-8---8-884079756898754034665052887678888669888983389876423679999862-678


Q ss_pred             CEEEEECCCC
Q ss_conf             5128988887
Q gi|254781064|r   90 SGFVFHNPNQ   99 (116)
Q Consensus        90 ~~F~~~NPna   99 (116)
                      ++|.+.+|--
T Consensus        77 ~~FSLE~p~G   86 (95)
T pfam05610        77 GMFSLEGPEG   86 (95)
T ss_pred             CEEEECCCCC
T ss_conf             7577148888


No 18 
>KOG4777 consensus
Probab=75.71  E-value=2.1  Score=23.33  Aligned_cols=44  Identities=23%  Similarity=0.354  Sum_probs=36.0

Q ss_pred             CCCEEEEECHHHHHHHCCCEEEEECCCCCCEEEEECCCCCCCCCC
Q ss_conf             468399997877320069899763177445128988887876788
Q gi|254781064|r   61 KDGVKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPNQVSACGC  105 (116)
Q Consensus        61 ~~g~~i~id~~s~~~L~g~~IDy~~~~~~~~F~~~NPna~~~CgC  105 (116)
                      .+++.++|+.-.-+.|++...-..+..|+.||+|.|||-+ +-+|
T Consensus       114 e~~VPLvvP~VNpehld~ik~~~~~~k~~~G~iI~nsNCS-Ta~~  157 (361)
T KOG4777         114 EDGVPLVVPEVNPEHLDGIKVGLDTGKMGKGAIIANSNCS-TAIC  157 (361)
T ss_pred             CCCCCEEECCCCHHHHHHHEECCCCCCCCCCEEEECCCCC-EEEE
T ss_conf             7997457334587784253022225888995289669887-0368


No 19 
>TIGR02176 pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxidoreductase; InterPro: IPR011895   The oxidative decarboxylation of pyruvate to acetyl-CoA, a central step in energy metabolism, can occur by two different mechanisms . In mitochondria and aerobic bacteria this reaction is catalysed by the multienzyme complex pyruvate dehydrogenase using NAD as electron acceptor. In anaerobic organisms, however, this reaction is reversibly catalysed by a single enzyme using either ferrodoxin or flavodoxin as the electron acceptor.   Pyruvate:ferrodoxin/flavodoxin reductases (PFORs) in this entry occur in both obligately and facultatively anaerobic bacteria and also some eukaryotic microorganisms. These proteins are single-chain enzymes containing a thiamin pyrophosphate cofactor for the cleavage of carbon-carbon bonds next to a carbonyl group, and iron-sulphur clusters for electron transfer. The Desulfovibrio africanus enzyme is currently the only PFOR whose three dimensional structure is known , . It is a homodimer where each subunit contains one thiamin pyrophosphate cofactor and two ferrodoxin-like 4Fe-S clusters and an atypical 4Fe-S cluster. Each monomer is composed of seven domains - domains I, II and VI make intersubunit contacts, while domains III, IV and V are located at the suface of the dimer, and domain VII forms a long arm extending over the other subunit. The cofactor is bound at the interface of domains I and VI and is proximal to the atypical 4Fe-S bound by domain VI, while the ferrodoxin-like 4Fe-S clusters are bound by domain V. Comparison of this enzyme with the multi-chain PFORs shows a correspondance between the domains in this enzyme and the subunits of the multi-chain enzymes.; GO: 0005506 iron ion binding, 0016903 oxidoreductase activity acting on the aldehyde or oxo group of donors, 0006118 electron transport.
Probab=53.06  E-value=21  Score=17.64  Aligned_cols=56  Identities=18%  Similarity=0.276  Sum_probs=27.3

Q ss_pred             CHHHHHHHHHHHHHCCC--CCCEEEE------EEECC----CCCCCEEEEHHHHCCCCCCCCEECCC-CEEEEE
Q ss_conf             68999999999971799--8618999------98479----87871132001100210122201246-839999
Q gi|254781064|r    8 TEAAVYRIKEIVFNSQG--KAQGIRI------SLKKG----GCAGLEYMVDLVTDNPVDGDDLIEKD-GVKVWI   68 (116)
Q Consensus         8 T~~A~~~i~~l~~~~~~--~~~~lRi------~v~~g----GC~G~~Y~l~~~~~~~~~~D~~~~~~-g~~i~i   68 (116)
                      |..+..+|+++|+.++-  +...=+|      .||.+    |=-||.|+++|     .--|+|+... +|+|+|
T Consensus       945 ~k~~~~klk~~L~~~k~~G~~ll~~i~~~~D~fvKkS~W~iGGDGWAYDIGY-----GGlDHVlASG~dVN~LV 1013 (1194)
T TIGR02176       945 SKERAAKLKKLLAGEKTKGDDLLKEIYAVKDLFVKKSVWIIGGDGWAYDIGY-----GGLDHVLASGKDVNVLV 1013 (1194)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCEEEEECCCCEEECCC-----CCCCCEEECCCCEEEEE
T ss_conf             9999999999998448886168986522026641331355537700131266-----73102021279601787


No 20 
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=52.09  E-value=6.6  Score=20.48  Aligned_cols=33  Identities=18%  Similarity=0.459  Sum_probs=20.6

Q ss_pred             CEEEEECC---CCCCE-EEEECCCCC-CCCCCCCCCCC
Q ss_conf             89976317---74451-289888878-76788521121
Q gi|254781064|r   79 TEIDFKTE---KLYSG-FVFHNPNQV-SACGCGQSVEI  111 (116)
Q Consensus        79 ~~IDy~~~---~~~~~-F~~~NPna~-~~CgCG~SF~~  111 (116)
                      -.+||.+.   ..|.. |+...|... .+|.||.||--
T Consensus        44 drv~~~dpillpvg~hlfi~qs~~~rv~rcecghsf~d   81 (165)
T COG4647          44 DRVDWDDPILLPVGDHLFICQSAQKRVIRCECGHSFGD   81 (165)
T ss_pred             HHCCCCCCEEEECCCEEEEEECCCCCEEEEECCCCCCC
T ss_conf             52366787465138807986666555788734665468


No 21 
>cd01531 Acr2p Eukaryotic arsenate resistance proteins are members of the Rhodanese Homology Domain superfamily. Included in this CD is the Saccharomyces cerevisiae arsenate reductase protein, Acr2p, and other yeast and plant homologs.
Probab=51.06  E-value=14  Score=18.68  Aligned_cols=20  Identities=10%  Similarity=0.125  Sum_probs=9.7

Q ss_pred             HHHHHHHHHCCCCCCEEEEEEE
Q ss_conf             9999999717998618999984
Q gi|254781064|r   13 YRIKEIVFNSQGKAQGIRISLK   34 (116)
Q Consensus        13 ~~i~~l~~~~~~~~~~lRi~v~   34 (116)
                      ++|++++++..  ...+-|.|.
T Consensus         7 ~~L~~~~~~~~--~~~~IIDvR   26 (113)
T cd01531           7 AQLKGWIRNGR--PPFQVVDVR   26 (113)
T ss_pred             HHHHHHHHCCC--CCEEEEECC
T ss_conf             99999997599--987999767


No 22 
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275   Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC).   Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.   Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains .    This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=46.51  E-value=8.9  Score=19.75  Aligned_cols=46  Identities=17%  Similarity=0.346  Sum_probs=27.8

Q ss_pred             EECHHHHHHHHHH-HHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCC
Q ss_conf             5268999999999-97179986189999847987871132001100210122201246
Q gi|254781064|r    6 TMTEAAVYRIKEI-VFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKD   62 (116)
Q Consensus         6 ~IT~~A~~~i~~l-~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~   62 (116)
                      |+||.=..+|++. ++=-      =-|+|.+|||| -||.|++    ......|++.|
T Consensus       254 TLtD~EYQ~LR~~sikII------R~lGi~GgGCN-vQFAL~P----~s~~Y~vIEvN  300 (1089)
T TIGR01369       254 TLTDKEYQMLRDASIKII------RELGIVGGGCN-VQFALDP----DSGRYYVIEVN  300 (1089)
T ss_pred             CCCCHHHHHHHHHHHHHH------HHCCCEECCCC-EEEEECC----CCCCEEEEEEC
T ss_conf             688078999999999999------87391216742-1321507----89706999867


No 23 
>TIGR01074 rep ATP-dependent DNA helicase Rep; InterPro: IPR005752    RepA hexameric DNA helicase contain ATP-binding domains similar to those seen in monomeric helicases but which are arranged in a ring. There is compelling evidence to suggest that a single ssDNA molecule passes through the centre of the hexameric ring. Activity of the enzyme is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilizing the duplex and separating the two strands in an active process  ; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=41.18  E-value=30  Score=16.79  Aligned_cols=68  Identities=24%  Similarity=0.271  Sum_probs=38.5

Q ss_pred             EEECHHHHHHHHHHHHHC--CCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEEEEECHHHHHHHCCCEE
Q ss_conf             652689999999999717--99861899998479878711320011002101222012468399997877320069899
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNS--QGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVKVWIDSASLLYMLGTEI   81 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~--~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~i~id~~s~~~L~g~~I   81 (116)
                      ||+|.+|+.++++.+++.  ..+..||-|+-       |. .|++-- =..|.+.+=-..|+.|+=+..+...|...+=
T Consensus        54 vTFTNKAA~EMkERVA~~L~~~~~~GL~isT-------FH-~LGL~I-i~~E~~~lG~K~nFSlFD~~D~~all~eL~~  123 (677)
T TIGR01074        54 VTFTNKAAREMKERVAKTLGKGQAKGLTIST-------FH-TLGLKI-IRREHNALGLKSNFSLFDETDQLALLKELLE  123 (677)
T ss_pred             EECCHHHHHHHHHHHHHHCCCCCCCCCEEEC-------CH-HHHHHH-HHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             7352377799999998522654558544752-------05-733899-9999986488999642067889999998752


No 24 
>COG4393 Predicted membrane protein [Function unknown]
Probab=37.32  E-value=38  Score=16.24  Aligned_cols=13  Identities=23%  Similarity=0.299  Sum_probs=5.1

Q ss_pred             EECHHHHHHHHHH
Q ss_conf             5268999999999
Q gi|254781064|r    6 TMTEAAVYRIKEI   18 (116)
Q Consensus         6 ~IT~~A~~~i~~l   18 (116)
                      +-+..|..+.++.
T Consensus       228 ~q~~~aI~krkk~  240 (405)
T COG4393         228 TQKNNAILKRKKA  240 (405)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             6401788999999


No 25 
>KOG0259 consensus
Probab=37.06  E-value=39  Score=16.19  Aligned_cols=73  Identities=25%  Similarity=0.424  Sum_probs=37.1

Q ss_pred             ECCCCC-CCEEEEHHHHCCCCCCCCEECCCCEEEE----------ECHHHHHHHCCCEEEEE--C---CCCCCEEEEECC
Q ss_conf             479878-7113200110021012220124683999----------97877320069899763--1---774451289888
Q gi|254781064|r   34 KKGGCA-GLEYMVDLVTDNPVDGDDLIEKDGVKVW----------IDSASLLYMLGTEIDFK--T---EKLYSGFVFHNP   97 (116)
Q Consensus        34 ~~gGC~-G~~Y~l~~~~~~~~~~D~~~~~~g~~i~----------id~~s~~~L~g~~IDy~--~---~~~~~~F~~~NP   97 (116)
                      -.+||+ +..+.++.. ..+..+ ..+-.-|+..|          |-+..+.-=++-+||+.  +   +...-..+++||
T Consensus       131 ltsGC~qAIe~~i~~L-A~p~aN-ILlPrPGfp~Y~~~a~~~~lEVR~ydlLPe~~weIDL~~veal~DENT~AivviNP  208 (447)
T KOG0259         131 LTSGCSQAIELAISSL-ANPGAN-ILLPRPGFPLYDTRAIYSGLEVRYYDLLPEKDWEIDLDGVEALADENTVAIVVINP  208 (447)
T ss_pred             EECCCHHHHHHHHHHH-CCCCCC-EECCCCCCCHHHHHHHHCCCEEEEECCCCCCCCEECHHHHHHHHCCCEEEEEEECC
T ss_conf             9556369999999974-389986-65479998468876632584367632567656153168899764467069999679


Q ss_pred             CCCCCCCCCCCCCCC
Q ss_conf             878767885211212
Q gi|254781064|r   98 NQVSACGCGQSVEIK  112 (116)
Q Consensus        98 na~~~CgCG~SF~~~  112 (116)
                      +-    .||.-|+-+
T Consensus       209 ~N----PcGnVys~~  219 (447)
T KOG0259         209 NN----PCGNVYSED  219 (447)
T ss_pred             CC----CCCCCCCHH
T ss_conf             99----986515199


No 26 
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.92  E-value=24  Score=17.35  Aligned_cols=35  Identities=11%  Similarity=0.095  Sum_probs=18.6

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC
Q ss_conf             652689999999999717998618999984798787
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAG   40 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G   40 (116)
                      +.|+.+-.+.+.+..++++.. .-.||.+.-|-=+|
T Consensus         4 ~Sia~sil~~v~~~a~~~g~~-~V~~V~l~IG~ls~   38 (135)
T PRK03824          4 WALAEAIVRTVLDYAQKEGAS-KVKALKVVLGELQD   38 (135)
T ss_pred             HHHHHHHHHHHHHHHHHCCCC-EEEEEEEEECCCCC
T ss_conf             999999999999999981997-59999999888464


No 27 
>COG0686 Ald Alanine dehydrogenase [Amino acid transport and metabolism]
Probab=32.25  E-value=46  Score=15.74  Aligned_cols=69  Identities=19%  Similarity=0.290  Sum_probs=40.1

Q ss_pred             HHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEECCCCEE--------EEECHHHHHHHCCCEEEEECCC
Q ss_conf             99997179986189999847987871132001100210122201246839--------9997877320069899763177
Q gi|254781064|r   16 KEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLIEKDGVK--------VWIDSASLLYMLGTEIDFKTEK   87 (116)
Q Consensus        16 ~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~~~~g~~--------i~id~~s~~~L~g~~IDy~~~~   87 (116)
                      ++++++=.+-..-+-|.+..|||  |.- .    .....+|-+++.+|+-        =.|.+.|..-|.++|+.|.=..
T Consensus       252 ~e~vk~MkpGsVivDVAiDqGGc--~Et-~----~~TTh~~PtY~~~gvvhY~VaNmPgaVprTst~AL~nat~py~l~l  324 (371)
T COG0686         252 REMVKQMKPGSVIVDVAIDQGGC--FET-S----HPTTHDDPTYEVDGVVHYGVANMPGAVPRTSTQALTNATLPYILQL  324 (371)
T ss_pred             HHHHHHCCCCCEEEEEEECCCCC--EEC-C----CCCCCCCCCEEECCEEEEECCCCCCCCCCHHHHHHHHCCHHHHHHH
T ss_conf             99997447985899998748881--530-4----5435789701635779996179986564145777640535889998


Q ss_pred             CCCE
Q ss_conf             4451
Q gi|254781064|r   88 LYSG   91 (116)
Q Consensus        88 ~~~~   91 (116)
                      .++|
T Consensus       325 a~~G  328 (371)
T COG0686         325 ADKG  328 (371)
T ss_pred             HCCH
T ss_conf             4131


No 28 
>TIGR02588 TIGR02588 conserved hypothetical protein TIGR02588; InterPro: IPR013417    The function of this protein is unknown. It is always found as part of a two-gene operon with IPR013416 from INTERPRO, a protein that appears to span the membrane seven times. It has so far been found in the bacteria Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus..
Probab=31.98  E-value=42  Score=15.96  Aligned_cols=67  Identities=16%  Similarity=0.282  Sum_probs=31.8

Q ss_pred             EEEEECCC----CCCCEEEEHHHHCCCCCCCCE--ECCCCEEEEECHHHHHHHCCCEEEEECCCC--CCEEEE-ECCCCC
Q ss_conf             99984798----787113200110021012220--124683999978773200698997631774--451289-888878
Q gi|254781064|r   30 RISLKKGG----CAGLEYMVDLVTDNPVDGDDL--IEKDGVKVWIDSASLLYMLGTEIDFKTEKL--YSGFVF-HNPNQV  100 (116)
Q Consensus        30 Ri~v~~gG----C~G~~Y~l~~~~~~~~~~D~~--~~~~g~~i~id~~s~~~L~g~~IDy~~~~~--~~~F~~-~NPna~  100 (116)
                      ||.|.+.|    -+| ||...|.-.+.. ....  +...+ .+-....+.+ --+.+|||..+.-  .+-|+| .||..-
T Consensus        35 ~l~v~~~ev~~~~~G-Qy~v~Fai~N~~-g~ta~~V~v~g-eL~~~e~~~E-~a~~~iDy~a~~~~~~G~liF~~dPr~G  110 (122)
T TIGR02588        35 VLIVAPAEVVREQDG-QYYVPFAIENRG-GKTAAAVEVKG-ELRQAEEVVE-EAEVTIDYLASGSKEKGTLIFRSDPRNG  110 (122)
T ss_pred             EEEEECCCEEECCCC-CEEEEEEEECCC-CCEEEHEEEEE-EEECCCCEEC-CCCCEEEECCCCCCCCCEEEEEECCCCC
T ss_conf             699974553760699-758788888178-97410557777-3313881420-4673798715997413068871289996


No 29 
>KOG3348 consensus
Probab=30.78  E-value=49  Score=15.59  Aligned_cols=37  Identities=22%  Similarity=0.466  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHH
Q ss_conf             999999999717998618999984798787113200110
Q gi|254781064|r   11 AVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVT   49 (116)
Q Consensus        11 A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~   49 (116)
                      +.+++.+++.+.= +...++|.=.++|| |.+|....+.
T Consensus         4 ~e~~l~~~L~~~l-~p~~v~V~D~SgGC-G~~F~v~IvS   40 (85)
T KOG3348           4 TEERLEELLTEAL-EPEHVEVQDVSGGC-GSMFDVVIVS   40 (85)
T ss_pred             HHHHHHHHHHHHC-CCEEEEEEECCCCC-CCEEEEEEEC
T ss_conf             6899999998344-84699999757986-6407899973


No 30 
>TIGR00636 PduO_Nterm ATP:cob(I)alamin adenosyltransferase; InterPro: IPR002779   ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) . Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type , EutT-type  and PduO-type . Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution.    This entry represents EutT- and PduO-type ATP:cob(I)alamin adenosyltransferases. PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation , while EutT produces AdoCbl for ethanolamine utilisation . ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid ac-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process.
Probab=30.60  E-value=26  Score=17.13  Aligned_cols=36  Identities=17%  Similarity=0.208  Sum_probs=30.4

Q ss_pred             CCEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCC
Q ss_conf             616526899999999997179986189999847987
Q gi|254781064|r    3 DIVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGC   38 (116)
Q Consensus         3 ~mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC   38 (116)
                      +.+.||++-...|.+.+.+-..+...|+-+|-|||-
T Consensus        84 ~~~~~~~e~V~~LE~~I~~Y~~~~~~l~~FvLPGGt  119 (184)
T TIGR00636        84 EPLKITEEDVKFLEERIDQYREELPPLKKFVLPGGT  119 (184)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             220005999999999999986531344306499962


No 31 
>PRK13696 hypothetical protein; Provisional
Probab=27.04  E-value=51  Score=15.52  Aligned_cols=19  Identities=16%  Similarity=0.310  Sum_probs=16.6

Q ss_pred             CCCCEEECHHHHHHHHHHH
Q ss_conf             9861652689999999999
Q gi|254781064|r    1 MSDIVTMTEAAVYRIKEIV   19 (116)
Q Consensus         1 M~~mi~IT~~A~~~i~~l~   19 (116)
                      |...|+|++.|.++|.++-
T Consensus         2 m~KTItIsddvY~~L~~iK   20 (72)
T PRK13696          2 MTKTITISDDVYEELLSIK   20 (72)
T ss_pred             CCEEEEECHHHHHHHHHHH
T ss_conf             7514653299999999885


No 32 
>pfam01155 HypA Hydrogenase expression/synthesis hypA family. Four conserved cysteines lie either side of the least conserved region.
Probab=26.64  E-value=39  Score=16.16  Aligned_cols=35  Identities=20%  Similarity=0.309  Sum_probs=18.5

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC
Q ss_conf             652689999999999717998618999984798787
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAG   40 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G   40 (116)
                      +.|+.+-.+.+.+..++++.. .-.+|.++-|-=+|
T Consensus         3 ~sia~~i~~~v~~~a~~~~~~-~V~~V~l~IG~ls~   37 (112)
T pfam01155         3 LSIAESIVEIVEEEAKENGAT-RVTRVRLEIGELSG   37 (112)
T ss_pred             HHHHHHHHHHHHHHHHHCCCC-EEEEEEEEECCCCC
T ss_conf             899999999999999982996-89999999888456


No 33 
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit; InterPro: IPR004232   Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site , . The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide , . Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols.    This entry represents the alpha subunit, which is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha.; GO: 0018822 nitrile hydratase activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process.
Probab=26.62  E-value=59  Score=15.17  Aligned_cols=29  Identities=28%  Similarity=0.430  Sum_probs=25.9

Q ss_pred             ECHHHHHHHHHHHHHCCCCCCEEEEEEEC
Q ss_conf             26899999999997179986189999847
Q gi|254781064|r    7 MTEAAVYRIKEIVFNSQGKAQGIRISLKK   35 (116)
Q Consensus         7 IT~~A~~~i~~l~~~~~~~~~~lRi~v~~   35 (116)
                      ||+.|.+|+.++.+++=++..|-||-.+.
T Consensus        16 I~~~avd~~~s~yene~gP~~GAkvVAka   44 (186)
T TIGR01323        16 ISEDAVDRLTSLYENEVGPENGAKVVAKA   44 (186)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCCEEEEEC
T ss_conf             98778999988875315856676689864


No 34 
>cd03377 TPP_PFOR_PNO Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as pyruvate NADP+ oxidoreductase (PNO). These enzymes are dependent on TPP and a divalent metal cation as cofactors. PFOR and PNO catalyze the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The PFOR from cyanobacterium Anabaena (NifJ) is required for the transfer of electrons from pyruvate to flavodoxin, which reduces nitrogenase. The facultative anaerobic mitochondrion of the photosynthetic protist Euglena gra
Probab=25.19  E-value=58  Score=15.20  Aligned_cols=28  Identities=18%  Similarity=0.381  Sum_probs=18.2

Q ss_pred             CCCEEEEHHHHCCCCCCCCEECCC-CEEEE-ECHH
Q ss_conf             871132001100210122201246-83999-9787
Q gi|254781064|r   39 AGLEYMVDLVTDNPVDGDDLIEKD-GVKVW-IDSA   71 (116)
Q Consensus        39 ~G~~Y~l~~~~~~~~~~D~~~~~~-g~~i~-id~~   71 (116)
                      -|+.|++++     .-.|+|+... +++|+ +|.+
T Consensus       160 DGWAYDIG~-----gGLdHVLAsG~nVNvLVlDtE  189 (365)
T cd03377         160 DGWAYDIGY-----GGLDHVLASGENVNILVLDTE  189 (365)
T ss_pred             CCHHHHCCC-----CHHHHHHHCCCCEEEEEECCC
T ss_conf             612320363-----115677745897289996586


No 35 
>KOG3580 consensus
Probab=24.09  E-value=31  Score=16.69  Aligned_cols=54  Identities=17%  Similarity=0.335  Sum_probs=33.6

Q ss_pred             CCCCCCEECCCC--EEEEECHHHHHHHCCCEEEEECCCCCCEEEEECCC-C-----CCCCCCCCCCCCC
Q ss_conf             101222012468--39999787732006989976317744512898888-7-----8767885211212
Q gi|254781064|r   52 PVDGDDLIEKDG--VKVWIDSASLLYMLGTEIDFKTEKLYSGFVFHNPN-Q-----VSACGCGQSVEIK  112 (116)
Q Consensus        52 ~~~~D~~~~~~g--~~i~id~~s~~~L~g~~IDy~~~~~~~~F~~~NPn-a-----~~~CgCG~SF~~~  112 (116)
                      ..++|+++.++.  +.=+|-.+.+.||.+.       ..|+..++..-. +     .-.||-|.||.|.
T Consensus       447 lqEGDQIL~VN~vdF~nl~REeAVlfLL~l-------PkGEevtilaQ~k~Dvyr~iv~s~vGDSFyIR  508 (1027)
T KOG3580         447 LQEGDQILKVNTVDFRNLVREEAVLFLLEL-------PKGEEVTILAQSKADVYRDIVASGVGDSFYIR  508 (1027)
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHHHHHCC-------CCCCEEEEHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             000362677536330104278889998628-------99767761343565899999862678605885


No 36 
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.79  E-value=39  Score=16.15  Aligned_cols=35  Identities=11%  Similarity=0.093  Sum_probs=20.7

Q ss_pred             EEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC
Q ss_conf             652689999999999717998618999984798787
Q gi|254781064|r    5 VTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAG   40 (116)
Q Consensus         5 i~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G   40 (116)
                      +.|+.+-.+.+.+..++++.. .-.||.++-|-=+|
T Consensus         4 lsi~~~iv~~v~~~a~~~~~~-~V~~v~l~iG~ls~   38 (117)
T PRK00564          4 YSVVSSLIALCEEHAKKNQAH-KIERVVVGIGERSA   38 (117)
T ss_pred             HHHHHHHHHHHHHHHHHCCCC-EEEEEEEEECCCCC
T ss_conf             999999999999999983997-79999999888552


No 37 
>TIGR01265 tyr_nico_aTase tyrosine/nicotianamine aminotransferases; InterPro: IPR005958   This entry describes tyrosine aminotransferase (2.6.1.5 from EC) as found in animals and Trypanosoma cruzi (Euglenozoa). It is the first enzyme of a pathway of tyrosine degradation via homogentisate.  L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway are included in this family. ; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding, 0006519 amino acid and derivative metabolic process.
Probab=21.96  E-value=62  Score=15.02  Aligned_cols=98  Identities=21%  Similarity=0.295  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHHHH-----CCCCCCE--EEEEEECCCCC-CCEEEEHHHHCCCCCCCCEECCCCEE----------EEECH
Q ss_conf             8999999999971-----7998618--99998479878-71132001100210122201246839----------99978
Q gi|254781064|r    9 EAAVYRIKEIVFN-----SQGKAQG--IRISLKKGGCA-GLEYMVDLVTDNPVDGDDLIEKDGVK----------VWIDS   70 (116)
Q Consensus         9 ~~A~~~i~~l~~~-----~~~~~~~--lRi~v~~gGC~-G~~Y~l~~~~~~~~~~D~~~~~~g~~----------i~id~   70 (116)
                      +.|.+.+.+.+++     ++.+..-  ==|. -.+||+ |.++.+.-....+.++ ..+-.=|+.          +-|-.
T Consensus        83 ~~AR~AvA~y~~~sfvhn~~~~~~l~a~DV~-ltsGCsqAIe~~I~aLA~~pG~N-ILvPRPGfP~Y~t~A~~~~lEvr~  160 (424)
T TIGR01265        83 LAAREAVAEYLSNSFVHNQRLPGKLSADDVV-LTSGCSQAIEIVIEALAQNPGAN-ILVPRPGFPLYDTRAAFSGLEVRL  160 (424)
T ss_pred             HHHHHHHHHHHHCCEEECCCCCCCCCCCCEE-EECCCHHHHHHHHHHHHCCCCCC-EECCCCCCCCHHHHHHHCCCCCCC
T ss_conf             7888999999662221257888875766448-84772268999999972689883-556877786689999771872000


Q ss_pred             HHH-HHHCCCEEEEEC-----CCCCCEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             773-200698997631-----774451289888878767885211212
Q gi|254781064|r   71 ASL-LYMLGTEIDFKT-----EKLYSGFVFHNPNQVSACGCGQSVEIK  112 (116)
Q Consensus        71 ~s~-~~L~g~~IDy~~-----~~~~~~F~~~NPna~~~CgCG~SF~~~  112 (116)
                      ..+ .==++=+||..+     |..-...+++|||-    -||.=|+=+
T Consensus       161 ydLdlPe~~WeiDL~~le~l~DekT~A~vv~NP~N----PCGsVF~~~  204 (424)
T TIGR01265       161 YDLDLPEKDWEIDLDGLESLADEKTVAIVVINPSN----PCGSVFSRD  204 (424)
T ss_pred             CCCCCCCCCCEECHHHHHHHHCCCCEEEEEECCCC----CCCCCCCHH
T ss_conf             24678887523647899876326876999847566----788887888


No 38 
>pfam12141 DUF3589 Protein of unknown function (DUF3589). This family of proteins is found in eukaryotes. Proteins in this family are typically between 541 and 717 amino acids in length. The function of this family is not known,
Probab=21.57  E-value=33  Score=16.55  Aligned_cols=20  Identities=25%  Similarity=0.572  Sum_probs=11.5

Q ss_pred             EEEEECCCCC-CCCCCCCCCC
Q ss_conf             1289888878-7678852112
Q gi|254781064|r   91 GFVFHNPNQV-SACGCGQSVE  110 (116)
Q Consensus        91 ~F~~~NPna~-~~CgCG~SF~  110 (116)
                      ..=|-=|.|- ..||||.+++
T Consensus       337 eiWvGfaRaHi~~CGCg~~mY  357 (488)
T pfam12141       337 EYWVGFARAHLKNCGCGKSMY  357 (488)
T ss_pred             EEEEEEHHHHHHCCCCCCCEE
T ss_conf             799977488543589988336


No 39 
>KOG0387 consensus
Probab=21.24  E-value=46  Score=15.79  Aligned_cols=98  Identities=18%  Similarity=0.177  Sum_probs=53.5

Q ss_pred             CEEECHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCEEEEHHHHCCCCCCCCEE---CCCCEEEEECHHHHHHHCC--
Q ss_conf             16526899999999997179986189999847987871132001100210122201---2468399997877320069--
Q gi|254781064|r    4 IVTMTEAAVYRIKEIVFNSQGKAQGIRISLKKGGCAGLEYMVDLVTDNPVDGDDLI---EKDGVKVWIDSASLLYMLG--   78 (116)
Q Consensus         4 mi~IT~~A~~~i~~l~~~~~~~~~~lRi~v~~gGC~G~~Y~l~~~~~~~~~~D~~~---~~~g~~i~id~~s~~~L~g--   78 (116)
                      -+.|.|+  .-|.+.+++-......+|+.+--+-|+|..|...-.   ...-|..+   ..-+..|+|-..+..++.|  
T Consensus       258 aLIVCP~--Tii~qW~~E~~~w~p~~rv~ilh~t~s~~r~~~~~~---~~~~~~~L~r~~~~~~~ilitty~~~r~~~d~  332 (923)
T KOG0387         258 ALIVCPA--TIIHQWMKEFQTWWPPFRVFILHGTGSGARYDASHS---SHKKDKLLIRKVATDGGILITTYDGFRIQGDD  332 (923)
T ss_pred             EEEECCH--HHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCHH---HHHHHHHHEEEECCCCCEEEEEHHHHCCCCCC
T ss_conf             5998248--899999999987476537999714776544443101---34431222035304684799742242004752


Q ss_pred             -CEEEEECCCCCCEEEEECCCCCCCCCCC
Q ss_conf             -8997631774451289888878767885
Q gi|254781064|r   79 -TEIDFKTEKLYSGFVFHNPNQVSACGCG  106 (116)
Q Consensus        79 -~~IDy~~~~~~~~F~~~NPna~~~CgCG  106 (116)
                       .-+.|.--.+.+|-.|.|||++-+=.|-
T Consensus       333 l~~~~W~y~ILDEGH~IrNpns~islack  361 (923)
T KOG0387         333 LLGILWDYVILDEGHRIRNPNSKISLACK  361 (923)
T ss_pred             CCCCCCCEEEECCCCCCCCCCCHHHHHHH
T ss_conf             34650347982376504698508999998


No 40 
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=21.09  E-value=61  Score=15.07  Aligned_cols=18  Identities=11%  Similarity=0.045  Sum_probs=6.5

Q ss_pred             CEEECHHHHHHHHHHHHH
Q ss_conf             165268999999999971
Q gi|254781064|r    4 IVTMTEAAVYRIKEIVFN   21 (116)
Q Consensus         4 mi~IT~~A~~~i~~l~~~   21 (116)
                      ++.-...++......++.
T Consensus       555 ~vv~~~~~a~~a~~~L~~  572 (1191)
T TIGR02168       555 VVVENLNAAKKAIAFLKQ  572 (1191)
T ss_pred             CCCCCHHHHHHHHHHHCC
T ss_conf             014897999999973110


No 41 
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5  bisphosphate containing liposomes. However,  membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding.  Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=20.08  E-value=68  Score=14.81  Aligned_cols=31  Identities=13%  Similarity=0.280  Sum_probs=19.3

Q ss_pred             CHHHHHHHCCCEEEEECC----------CCCCEEEEECCCC
Q ss_conf             787732006989976317----------7445128988887
Q gi|254781064|r   69 DSASLLYMLGTEIDFKTE----------KLYSGFVFHNPNQ   99 (116)
Q Consensus        69 d~~s~~~L~g~~IDy~~~----------~~~~~F~~~NPna   99 (116)
                      +|.-++-|+|-||||.+.          ..|++|-|+.-++
T Consensus        45 eP~E~mqLdGyTVDY~e~~~~~~~~~~~l~ggr~FF~aVkE   85 (117)
T cd01234          45 EPTEFIQLDGYTVDYMPESDPDPNSELSLQGGRHFFNAVKE   85 (117)
T ss_pred             CHHHHHEECCEEEECCCCCCCCCCCCCCCCCCCEEEEEECC
T ss_conf             80675212554773357888665444345464210011115


Done!