Query         gi|254781220|ref|YP_003065633.1| hypothetical protein CLIBASIA_05635 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 130
No_of_seqs    2 out of 4
Neff          1.5 
Searched_HMMs 39220
Date          Mon May 30 07:05:07 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781220.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam08549 SWI-SNF_Ssr4 Fungal   60.6      11 0.00029   19.2   3.4   59   51-112   361-435 (669)
  2 pfam08926 DUF1908 Domain of un  48.8      24 0.00061   17.1   4.7   64   32-104   186-251 (282)
  3 TIGR01258 pgm_1 phosphoglycera  40.7      25 0.00065   16.9   2.6   30   26-59     45-74  (248)
  4 TIGR01051 topA_bact DNA topois  38.7      23 0.00058   17.3   2.1   43   35-77    320-364 (688)
  5 pfam06238 Borrelia_lipo_2 Borr  35.4      39 0.00099   15.8   4.4   38   45-82     30-93  (111)
  6 COG3525 Chb N-acetyl-beta-hexo  34.2      11 0.00028   19.3  -0.1   33   68-100   276-308 (732)
  7 pfam09363 XFP_C XFP C-terminal  31.3      45  0.0011   15.3   4.3   57   53-115   143-199 (203)
  8 TIGR01070 mutS1 DNA mismatch r  28.6      29 0.00075   16.5   1.3   50   40-89    219-271 (863)
  9 cd03066 PDI_b_Calsequestrin_mi  21.6     6.5 0.00016   20.8  -3.1   56   34-96      9-70  (102)
 10 PHA01634 hypothetical protein   20.7      34 0.00086   16.1   0.4   10  104-113    97-106 (156)
 11 TIGR02769 nickel_nikE nickel i  20.4      33 0.00085   16.2   0.3   27   19-45     99-125 (267)

No 1  
>pfam08549 SWI-SNF_Ssr4 Fungal domain of unknown function (DUF1750). This is a fungal domain of unknown function.
Probab=60.63  E-value=11  Score=19.21  Aligned_cols=59  Identities=27%  Similarity=0.358  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHH----HCCHHHHHHHHHHHHCCCCHHH
Q ss_conf             8999986446788879------------999999999999998787788887----4101466543444312777035
Q gi|254781220|r   51 KLIHFRDRTIRTHILE------------DLIEEVNRIIVLAKAHKRRLELKI----FEDNEVWRLLDEAREDCEGCEN  112 (130)
Q Consensus        51 ~~i~~~~Rt~~T~i~~------------D~~ee~~~~I~L~kA~~r~L~~~i----fed~E~WrlldE~~~D~E~~E~  112 (130)
                      |.-.|+||....+-+.            -.|+..||.-.|.+|-+ +|.-..    =-..|+|||  |-|+|....|+
T Consensus       361 kAeeF~~RV~~kva~~~aEIEkmKa~Hakrm~Kfkr~s~l~~AE~-~LR~a~~dp~~~G~E~WRl--EGr~~~~~ee~  435 (669)
T pfam08549       361 VADEFADRVAKKVADMTAEIEKLKKRHARRMEKFNRTSALKDAEQ-RLRDAAADPADTGSEIWRL--EGRLEIDTEDD  435 (669)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH-HHHHHHCCHHHCCCCCEEE--CCCCCCCCCCC
T ss_conf             899999999998888899999999999999998630027888999-9887405854337500242--35225765567


No 2  
>pfam08926 DUF1908 Domain of unknown function (DUF1908). This domain is found in a set of hypothetical/structural eukaryotic proteins.
Probab=48.81  E-value=24  Score=17.09  Aligned_cols=64  Identities=33%  Similarity=0.446  Sum_probs=41.3

Q ss_pred             CCEEHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             50111578879999997488999986446--78887999999999999999878778888741014665434443
Q gi|254781220|r   32 SNYEVEVIEKLERALKTSKKLIHFRDRTI--RTHILEDLIEEVNRIIVLAKAHKRRLELKIFEDNEVWRLLDEAR  104 (130)
Q Consensus        32 ~~~E~ev~E~Le~~l~~~~~~i~~~~Rt~--~T~i~~D~~ee~~~~I~L~kA~~r~L~~~ifed~E~WrlldE~~  104 (130)
                      +.|=.|++|||++-|-      +...||.  .+-....+|..+--||   ---||-||-+-|.-.|++.||..+.
T Consensus       186 s~YFyElsE~LEkLL~------Ea~ekSe~e~~~~i~~lvkKLL~II---SRPARLLECLEFDPeEFY~lLEaaE  251 (282)
T pfam08926       186 SRYFYELQEKLERLLH------EAKERSESEEVAEITGLVKKLLIII---SRPARLLECLEFDPEEFYHLLEAAE  251 (282)
T ss_pred             HHHHHHHHHHHHHHHH------HHHHCCCHHHHHHHHHHHHHHHHEE---CCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             6999999999999999------9885045778899999998888301---4658888887279899999999875


No 3  
>TIGR01258 pgm_1 phosphoglycerate mutase 1 family; InterPro: IPR005952    Most members of this family are phosphoglycerate mutase (5.4.2.1 from EC). This enzyme interconverts 2-phosphoglycerate and 3-phosphoglycerate.  2-phospho-D-glycerate + 2,3-diphosphoglycerate = 3-phospho-D-glycerate + 2,3-diphosphoglycerate. The enzyme is transiently phosphorylated on an active site histidine by 2,3-diphosphoglyerate, which is both substrate and product. Some members of this family have are phosphoglycerate mutase as a minor activity and act primarily as a bisphoglycerate mutase, interconverting 2,3-diphosphoglycerate and 1,3-diphosphoglycerate (5.4.2.4 from EC). ; GO: 0016868 intramolecular transferase activity phosphotransferases, 0006096 glycolysis.
Probab=40.74  E-value=25  Score=16.93  Aligned_cols=30  Identities=27%  Similarity=0.315  Sum_probs=21.7

Q ss_pred             CCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4688865011157887999999748899998644
Q gi|254781220|r   26 MGIEPESNYEVEVIEKLERALKTSKKLIHFRDRT   59 (130)
Q Consensus        26 mgiePe~~~E~ev~E~Le~~l~~~~~~i~~~~Rt   59 (130)
                      -|++||+-|    .-.|-|||.|++-+.+.-||+
T Consensus        45 ~g~~FD~ay----TS~LkRAI~Tl~~~L~~ldq~   74 (248)
T TIGR01258        45 EGYEFDIAY----TSLLKRAIHTLNIVLDELDQL   74 (248)
T ss_pred             CCCCCCEEE----HHHHHHHHHHHHHHHHHHCCE
T ss_conf             599876211----012678999999999985880


No 4  
>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.     This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place.    More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=38.75  E-value=23  Score=17.27  Aligned_cols=43  Identities=14%  Similarity=0.224  Sum_probs=26.2

Q ss_pred             EHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             115788799999974889999--8644678887999999999999
Q gi|254781220|r   35 EVEVIEKLERALKTSKKLIHF--RDRTIRTHILEDLIEEVNRIIV   77 (130)
Q Consensus        35 E~ev~E~Le~~l~~~~~~i~~--~~Rt~~T~i~~D~~ee~~~~I~   77 (130)
                      -|+|--+|=|.+++-...|-+  .-|||||.|-++|++++..+|.
T Consensus       320 TM~iAQ~LYEGv~~~~~~~G~ITYMRTDS~~lS~~A~~eaR~~I~  364 (688)
T TIGR01051       320 TMMIAQRLYEGVSLGEGTVGLITYMRTDSTRLSNEAVNEARNLID  364 (688)
T ss_pred             HHHHHHHHHCCEECCCCEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             655542331254438955899832863305789999999998888


No 5  
>pfam06238 Borrelia_lipo_2 Borrelia burgdorferi BBR25 lipoprotein. This family consists of a number of lipoproteins from the Lyme disease spirochete Borrelia burgdorferi.
Probab=35.35  E-value=39  Score=15.75  Aligned_cols=38  Identities=32%  Similarity=0.406  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHH-----------HHHHHHHHHHH---------------HHHHHHHHHHHH
Q ss_conf             999748899998644-----------67888799999---------------999999999987
Q gi|254781220|r   45 ALKTSKKLIHFRDRT-----------IRTHILEDLIE---------------EVNRIIVLAKAH   82 (130)
Q Consensus        45 ~l~~~~~~i~~~~Rt-----------~~T~i~~D~~e---------------e~~~~I~L~kA~   82 (130)
                      -+.|-++|||||-.+           .|+-|.+..-|               .-+++|+.+||.
T Consensus        30 yintf~~vidffyktyi~tlksme~aES~kif~eiqdilk~nieiieaist~k~kriisslkak   93 (111)
T pfam06238        30 YINTFSKVIDFFYKTYISTLKSMETAESTKIFEEIKDILKYNIEIIEAISTDKNKKIITSLKAK   93 (111)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             8888999999999999988999888899999999999997047778687426517899999998


No 6  
>COG3525 Chb N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism]
Probab=34.20  E-value=11  Score=19.30  Aligned_cols=33  Identities=33%  Similarity=0.446  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             999999999999987877888874101466543
Q gi|254781220|r   68 LIEEVNRIIVLAKAHKRRLELKIFEDNEVWRLL  100 (130)
Q Consensus        68 ~~ee~~~~I~L~kA~~r~L~~~ifed~E~Wrll  100 (130)
                      -.++++++|-.+.|||-|---+-..|+|-||+-
T Consensus       276 s~~~vk~~Id~laa~Kln~~hlHLtddegwrle  308 (732)
T COG3525         276 STDDVKRLIDQLAAHKLNVLHLHLTDDEGWRLE  308 (732)
T ss_pred             CHHHHHHHHHHHHHHHCCEEEEEECCCCCEEEC
T ss_conf             799999999998875246578754067421430


No 7  
>pfam09363 XFP_C XFP C-terminal domain. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22.
Probab=31.33  E-value=45  Score=15.33  Aligned_cols=57  Identities=25%  Similarity=0.279  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             999864467888799999999999999987877888874101466543444312777035673
Q gi|254781220|r   53 IHFRDRTIRTHILEDLIEEVNRIIVLAKAHKRRLELKIFEDNEVWRLLDEAREDCEGCENCSE  115 (130)
Q Consensus        53 i~~~~Rt~~T~i~~D~~ee~~~~I~L~kA~~r~L~~~ifed~E~WrlldE~~~D~E~~E~~~E  115 (130)
                      ..++.+++|-|+-.|+++-+-+.-..+.+-...+..++-+-+.|-      ++.|+|-.++..
T Consensus       143 M~v~N~~dRfhLa~dai~~~~~~~~~~~~~~~~~~~~l~~h~~yi------~e~G~D~pei~~  199 (203)
T pfam09363       143 MRVLNELDRFHLAIDAIDRVPRLGDKAAALKQEMDDKLIEHRQYI------REHGEDMPEIRD  199 (203)
T ss_pred             HHHHCCCCHHHHHHHHHHHCHHCCHHHHHHHHHHHHHHHHHHHHH------HHHCCCCHHHHC
T ss_conf             887707668999999999652001559999999999999999999------996899536518


No 8  
>TIGR01070 mutS1 DNA mismatch repair protein MutS; InterPro: IPR005748   Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA.    MutS is a modular protein with a complex structure , and is composed of:    N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts.    Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts .    This entry represents a family of MutS proteins.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair.
Probab=28.65  E-value=29  Score=16.53  Aligned_cols=50  Identities=28%  Similarity=0.379  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             879999997488999986446788879---99999999999999878778888
Q gi|254781220|r   40 EKLERALKTSKKLIHFRDRTIRTHILE---DLIEEVNRIIVLAKAHKRRLELK   89 (130)
Q Consensus        40 E~Le~~l~~~~~~i~~~~Rt~~T~i~~---D~~ee~~~~I~L~kA~~r~L~~~   89 (130)
                      ++...++++.-+|.-.-+||-+|-|.-   =-+.+..-.|-|..|++|||++.
T Consensus       219 ~~~~~~~~A~g~LL~Ya~~TQ~~~L~Hl~p~~~~~~~d~~~ld~At~rnLEl~  271 (863)
T TIGR01070       219 RNAPLGLKAAGCLLQYAKRTQRTALPHLRPVRLYELQDFVQLDAATRRNLELT  271 (863)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECHHHHHHHHHHHHHHHCCC
T ss_conf             23403667888999999986102443036302455487773578876531000


No 9  
>cd03066 PDI_b_Calsequestrin_middle PDIb family, Calsequestrin subfamily, Middle TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca
Probab=21.58  E-value=6.5  Score=20.79  Aligned_cols=56  Identities=29%  Similarity=0.384  Sum_probs=42.3

Q ss_pred             EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH----HHHHHHHHHHHHHHCCHHH
Q ss_conf             111578879999997488999986446788879--99999999999----9998787788887410146
Q gi|254781220|r   34 YEVEVIEKLERALKTSKKLIHFRDRTIRTHILE--DLIEEVNRIIV----LAKAHKRRLELKIFEDNEV   96 (130)
Q Consensus        34 ~E~ev~E~Le~~l~~~~~~i~~~~Rt~~T~i~~--D~~ee~~~~I~----L~kA~~r~L~~~ifed~E~   96 (130)
                      -|++--+++|+    +-+||.+|+--+|.|..+  ||-++...+|.    .-+..||.|.||+   |||
T Consensus         9 ~el~~F~~~ee----diklIGyFk~~~S~hy~~F~eAAe~F~P~IkFfAtf~~kvAk~L~LK~---neV   70 (102)
T cd03066           9 RELQAFENIED----DIKLIGYFKSEDSEHYKAFEEAAEEFHPYIKFFATFDSKVAKKLGLKM---NEV   70 (102)
T ss_pred             HHHHHHHHHHH----CEEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHCCCC---CCE
T ss_conf             78888763021----157888744898668999999998636623566564588998837600---415


No 10 
>PHA01634 hypothetical protein
Probab=20.75  E-value=34  Score=16.14  Aligned_cols=10  Identities=60%  Similarity=1.185  Sum_probs=7.0

Q ss_pred             HHCCCCHHHH
Q ss_conf             3127770356
Q gi|254781220|r  104 REDCEGCENC  113 (130)
Q Consensus       104 ~~D~E~~E~~  113 (130)
                      -.||||||+-
T Consensus        97 vmDCEGCEe~  106 (156)
T PHA01634         97 VMDCEGCEEK  106 (156)
T ss_pred             EEECCCHHHH
T ss_conf             9976463764


No 11 
>TIGR02769 nickel_nikE nickel import ATP-binding protein NikE; InterPro: IPR014137   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase..
Probab=20.45  E-value=33  Score=16.17  Aligned_cols=27  Identities=26%  Similarity=0.325  Sum_probs=15.5

Q ss_pred             HHCCCCCCCCCCCCCEEHHHHHHHHHH
Q ss_conf             637883246888650111578879999
Q gi|254781220|r   19 LSAVNPRMGIEPESNYEVEVIEKLERA   45 (130)
Q Consensus        19 ~S~~N~rmgiePe~~~E~ev~E~Le~~   45 (130)
                      .|+|||||.|+--|.=-|+-.+.|+++
T Consensus        99 ~savNPr~tv~~ii~EPLrhl~~L~~s  125 (267)
T TIGR02769        99 PSAVNPRKTVREIIGEPLRHLTSLDES  125 (267)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             431162578999986257766548899


Done!