HHsearch alignment for GI: 254780382 and conserved domain: TIGR00963

>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=99.53  E-value=5.1e-14  Score=109.31  Aligned_cols=280  Identities=17%  Similarity=0.249  Sum_probs=168.6

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             79878989999999997699799982798517899999999998606521478279998285899999999987410233
Q gi|254780382|r   20 GYVKPTPIQIKTIPLVLQRHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRMPRTLILEPTRELAAQVADNFEKYGKNY   99 (465)
Q Consensus        20 ~~~~pt~iQ~~~i~~~l~g~dvi~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~~~~~~   99 (465)
T Consensus        58 G~r-~fDVQliGg~~LH~G~--IAEMkTGEGKTL~AtLpaYLNAL~Gk----G--VHvVTVNdYLA~RD~e~m~~v~~FL  128 (904)
T TIGR00963        58 GLR-PFDVQLIGGIVLHKGK--IAEMKTGEGKTLVATLPAYLNALTGK----G--VHVVTVNDYLARRDAEWMGQVYRFL  128 (904)
T ss_pred             CCC-CHHHHHHHHHHHCCCC--EEEECCCCCHHHHHHHHHHHHHHCCC----C--CEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             785-6189999999980896--67831488628999999998765179----6--2799635044488899878999684


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCHH-HHHHHCC------CCCCCCCEEECCCCCCCCC-CC----------
Q ss_conf             3221000012222222222210112210221023-3332000------0001210010255100000-00----------
Q gi|254780382|r  100 NLTVALLIGGIPFEAQNKKLERGADVLICTPGRI-LDHFNRG------KLLMNNIEILVIDEADRML-DM----------  161 (465)
Q Consensus       100 ~l~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rl-~~~l~~~------~~~l~~~~~lViDEah~l~-~~----------  161 (465)
T Consensus       129 GL~VGl~~~~m~~~eR--r~aY~cDITY~TNnELGFDYLRDNM~~~~ee~vqR~f~FAIIDEVDSILIDEARTPLIISGp  206 (904)
T TIGR00963       129 GLSVGLILSSMSPEER--REAYACDITYGTNNELGFDYLRDNMALSKEEKVQRPFNFAIIDEVDSILIDEARTPLIISGP  206 (904)
T ss_pred             CCEEEEECCCCCHHHH--HHHHCCCEEEECCCCCCHHHHHHHHHCCHHHHHCCCCCCEEEEEECCEEECCCCCCCCCCCC
T ss_conf             9368886179985899--99854981653265420246667641150121016722268864244642333686523576


Q ss_pred             ------CCH---------------HHHHHHHHHHC-C-CC--------CCCCCCCC---C-CCCC---C-------CCCC
Q ss_conf             ------100---------------35788754310-2-22--------22333432---1-1222---2-------1111
Q gi|254780382|r  162 ------GFI---------------PYIQNITSLVP-F-TR--------QTLLFSAT---M-TDEL---Q-------KVSE  196 (465)
Q Consensus       162 ------gf~---------------~~i~~i~~~~~-~-~~--------q~i~~SAT---~-~~~v---~-------~l~~  196 (465)
T Consensus       207 ae~~~~~Y~ev~~~~~~l~e~~~~p~a~~~~~~l~e~W~~dY~vDeK~r~v~Lte~G~~~WaE~~L~~~g~~~~~~nLyd  286 (904)
T TIGR00963       207 AEKSTEKYLEVNKLVDPLKETDKLPQANEVAKALKEKWDVDYEVDEKNRNVLLTEKGMKKWAEDLLGVDGIIKGAVNLYD  286 (904)
T ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCEEECCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCHH
T ss_conf             67863010017878866416655750445689986311677035104174651401178999875324321443013012


Q ss_pred             ------------------CCCCCCC------------------------------------CCCCCCCCCCCCCCC----
Q ss_conf             ------------------2222210------------------------------------013444321234642----
Q gi|254780382|r  197 ------------------NFLQNPK------------------------------------RIEVNTPSSTAETIE----  218 (465)
Q Consensus       197 ------------------~~l~~~~------------------------------------~i~v~~~~~~~~~i~----  218 (465)
T Consensus       287 ~~n~~~~hyi~nALkA~~lf~kDvdYIV~dgeV~IVDEFTGRim~GRR~SdGLHQAiEAKE~V~I~~En~T~AtITyQNf  366 (904)
T TIGR00963       287 LENSPLIHYILNALKAKELFEKDVDYIVRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNF  366 (904)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHCCCEEECCCCEEEEHHHHHH
T ss_conf             45334588899999999987439835888887899873058338896124225799997468601035522440445767


Q ss_pred             ------------------------------------------CCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCC
Q ss_conf             ------------------------------------------11111222211024443210122345650677621344
Q gi|254780382|r  219 ------------------------------------------HCFVATYAQYSKKCALLQQLLQSQDTMKNGIIFCNQKK  256 (465)
Q Consensus       219 ------------------------------------------~~~~~~~~~~~~k~~~l~~l~~~~~~~~k~iIF~~t~~  256 (465)
T Consensus       367 FrlY~KLsGMTGTA~TE~~EF~~IYnL~Vv~vPTNrp~~R~D~~DlvY~te~~Kw~Av~~e~~~~h~~GqPvLvGT~svE  446 (904)
T TIGR00963       367 FRLYEKLSGMTGTAKTEEEEFEKIYNLEVVVVPTNRPVIRKDLPDLVYKTEEEKWKAVVDEIKEIHAKGQPVLVGTTSVE  446 (904)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHHHCCCCEEEEECCHH
T ss_conf             65426544687756899998404577513551667723446777734647688999999999998746898777522177


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCHHHHHH-HHHHHCCCCCEEEEEHHHHHHHHCC
Q ss_conf             322222222223322222345420333234-4442013552388884664644078
Q gi|254780382|r  257 NVVNLCHSLEKQGFSVCAIHGNIDQRSRMK-ILSNFKEGTIQLMVASDLAARGLDI  311 (465)
Q Consensus       257 ~~~~l~~~L~~~g~~v~~lhg~l~~~~R~~-~~~~F~~g~~~vLV~Td~~~~GiDi  311 (465)
T Consensus       447 ~SE~LS~lL~~~~I~H~VLNAKPENh~rEAeIia~-AG~kGAVTIATNMAGRGTDI  501 (904)
T TIGR00963       447 KSELLSKLLKERGIPHNVLNAKPENHEREAEIIAQ-AGRKGAVTIATNMAGRGTDI  501 (904)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH-CCCCCCEEEEECCCCCCCCE
T ss_conf             78999999985789812247874467789999996-08886416762478776450