HHsearch alignment for GI: 254780619 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=95.05  E-value=0.12  Score=31.68  Aligned_cols=265  Identities=18%  Similarity=0.196  Sum_probs=143.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH---HHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEE
Q ss_conf             75315799999999998514684799715210013---445554303897689962355723566789999719973999
Q gi|254780619|r  226 VTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTS---AILERFQKRFGVKPAEWHSSLSTSMREKIWRQVARGAISVIV  302 (731)
Q Consensus       226 vTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~---Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i~~G~~~IVI  302 (731)
T Consensus        81 kTGEGKTL~AtLpaYLNAL~GkGVHvVTVNdYLA~RD~e~m~~v~~FLGL~VGl~~~~m~~~eRr~aY~------cDITY  154 (904)
T TIGR00963        81 KTGEGKTLVATLPAYLNALTGKGVHVVTVNDYLARRDAEWMGQVYRFLGLSVGLILSSMSPEERREAYA------CDITY  154 (904)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHC------CCEEE
T ss_conf             148862899999999876517962799635044488899878999684936888617998589999854------98165


Q ss_pred             EC----------------------CHHHHHHHCCCEEEEEEE-----------C-CCCCCH-----------HCCCCCCC
Q ss_conf             40----------------------012110010001367740-----------5-532100-----------00244322
Q gi|254780619|r  303 GV----------------------RSALFLPFKKLGLIVIDE-----------E-HDISYK-----------QEEGILYN  337 (731)
Q Consensus       303 Gt----------------------RSAif~P~~nLglIIvDE-----------E-Hd~syk-----------q~~~pry~  337 (731)
T Consensus       155 ~TNnELGFDYLRDNM~~~~ee~vqR~f~FAIIDEVDSILIDEARTPLIISGpae~~~~~Y~ev~~~~~~l~e~~~~p--~  232 (904)
T TIGR00963       155 GTNNELGFDYLRDNMALSKEEKVQRPFNFAIIDEVDSILIDEARTPLIISGPAEKSTEKYLEVNKLVDPLKETDKLP--Q  232 (904)
T ss_pred             ECCCCCCHHHHHHHHHCCHHHHHCCCCCCEEEEEECCEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCC--C
T ss_conf             32654202466676411501210167222688642446423336865235766786301001787886641665575--0


Q ss_pred             HHHHHHHHH-H-HCCCC-------EE-------C-CCCCCCHH-------HHHHHHHH-HHHHHC----------CCCCC
Q ss_conf             489999975-1-10321-------00-------0-02454324-------67753212-344412----------43223
Q gi|254780619|r  338 ARDMSIVRG-K-IESFP-------VV-------L-VSATPSIE-------SRVNGISR-RYHSVH----------LSTRY  382 (731)
Q Consensus       338 aRdvA~~Ra-~-~~~~~-------li-------l-gSATPSle-------s~~~~~~g-~~~~~~----------l~~R~  382 (731)
T Consensus       233 a~~~~~~l~e~W~~dY~vDeK~r~v~Lte~G~~~WaE~~L~~~g~~~~~~nLyd~~n~~~~hyi~nALkA~~lf~kDvdY  312 (904)
T TIGR00963       233 ANEVAKALKEKWDVDYEVDEKNRNVLLTEKGMKKWAEDLLGVDGIIKGAVNLYDLENSPLIHYILNALKAKELFEKDVDY  312 (904)
T ss_pred             HHHHHHHHHHHCCCCCEEECCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             44568998631167703510417465140117899987532432144301301245334588899999999987439835


Q ss_pred             CCCCCCCCEECCC-CCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCEEHHCCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             6765433211022-223322245479899999988622655179974222000000235654343101465201211357
Q gi|254780619|r  383 RNSALPHLQVIDM-RGQTIAQGKSLSPEMIDGIRHTLARNEQTLLFLNRRGYAPLTLCQVCGNRLKCLHCSCWLVEHRSK  461 (731)
Q Consensus       383 ~~~~~P~i~ivDm-~~~~~~~~~~lS~~l~~~i~~~l~~g~qvll~lnRrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~  461 (731)
T Consensus       313 IV-~dgeV~IVDEFTGRim-~GRR~SdGLHQAi----EAKE~V~I~~En~T~At-------------------ITy---Q  364 (904)
T TIGR00963       313 IV-RDGEVVIVDEFTGRIM-EGRRWSDGLHQAI----EAKEGVEIQNENQTLAT-------------------ITY---Q  364 (904)
T ss_pred             EE-ECCEEEEEEEECCCCC-CCCCCCCHHHHHH----HHHCCCEEECCCCEEEE-------------------HHH---H
T ss_conf             88-8887899873058338-8961242257999----97468601035522440-------------------445---7


Q ss_pred             CCCEECHHHCCCCCCCCCCCCCCCCEECCCCCCHHHHHH-HHHHCC-------CC-CHHHHCCC-CC--CCCHHHHHHH-
Q ss_conf             832000021024465556667874110013542899888-852048-------52-00010232-11--3586789999-
Q gi|254780619|r  462 KKLYCHQCGHSAIYSQSCVVCGSSGKMIACGFGIERIAE-EVCEYF-------PL-ARISILSS-DL--EGGGGRLQLQ-  528 (731)
Q Consensus       462 ~~l~Ch~Cg~~~~~~~~Cp~Cg~~~~l~~~G~Gte~~~e-~l~~~f-------p~-~~v~~~d~-d~--~~~~~~~~~~-  528 (731)
T Consensus       365 Nf------------FrlY------~KLsGM-TGTA~TE~~EF~~IYnL~Vv~vPTNrp~~R~D~~DlvY~te~~Kw~Av~  425 (904)
T TIGR00963       365 NF------------FRLY------EKLSGM-TGTAKTEEEEFEKIYNLEVVVVPTNRPVIRKDLPDLVYKTEEEKWKAVV  425 (904)
T ss_pred             HH------------HHHH------HHHCCC-CCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCEECCHHHHHHHHH
T ss_conf             67------------6542------654468-7756899998404577513551667723446777734647688999999


Q ss_pred             ---HHHHCCCCCCEEEEEHHH
Q ss_conf             ---986212576579870443
Q gi|254780619|r  529 ---LSAIAKGEIDIIIGTQLV  546 (731)
Q Consensus       529 ---~~~~~~~~~~ilvgTq~i  546 (731)
T Consensus       426 ~e~~~~h~~GqP-vLvGT~sv  445 (904)
T TIGR00963       426 DEIKEIHAKGQP-VLVGTTSV  445 (904)
T ss_pred             HHHHHHHHCCCC-EEEEECCH
T ss_conf             999998746898-77752217