Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate WP_090439677.1 BLS63_RS03195 Tat pathway signal protein
Query= TCDB::Q9FA44 (504 letters) >NCBI__GCF_900100495.1:WP_090439677.1 Length = 506 Score = 338 bits (867), Expect = 3e-97 Identities = 177/484 (36%), Positives = 285/484 (58%), Gaps = 8/484 (1%) Query: 7 LSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILL 66 L QGF + L++ +IG VG + G +PGL VA+ LPL F + ++ L LL Sbjct: 5 LQQGFGAVFSLNILLLMVIGVAVGIVFGAVPGLSATMAVALCLPLTFTMG--PQAGLSLL 62 Query: 67 ATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIA 126 ++IG GG IS+ILL +PG ++I T DG P+ +QG G AL I V SF G+L + Sbjct: 63 VALFIGATSGGLISAILLKIPGTPSSIATVFDGGPLMEQGHGVKALGIGIVFSFLGTLFS 122 Query: 127 IGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGV 186 I ++ AP LA+ +L FGP EYFA+ VF++ + ++ A + +K A +G ++TVG+ Sbjct: 123 IAALMFIAPQLAKVALRFGPHEYFAIAVFSLTLIATLSAGSMVKGLFAGALGFAVSTVGI 182 Query: 187 DANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLE-----HTSSGQTMVRKTGRM 241 + RFTFD L+ G + V+IG+F+V+EI+ + E H Q++ K + Sbjct: 183 APVEAIRRFTFDVAELNGGFAMLTVMIGMFAVAEIIKVAESGRHAHQGKAQSVSMKNIKG 242 Query: 242 L-FNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIR 300 F+LKE + + RS +IG +G+LPG GA ++ + Y+ KK + + +++GKG+I Sbjct: 243 FGFSLKEFREQLPNAGRSGLIGLGIGILPGIGAGTSNLVAYIISKKRAKHPETYGKGNIG 302 Query: 301 GVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGL 360 GV A E ANNA G+ +P++TLG+PG TA+++G ++ I PGP +F Q +V+ + Sbjct: 303 GVVASETANNAGIGGAMLPLMTLGIPGDTVTAILLGGFLIHGIQPGPLLFISQGPLVYTI 362 Query: 361 IAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVA 420 AAL+++ V++L M + LF ++L +P ++P I + VG + + S FD+ ++ Sbjct: 363 FAALIVSTVLMLFMEFYGLRLFIKLLDVPKHILLPIILVLCVVGAFGLSSRLFDVWSILV 422 Query: 421 LGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMAI 480 G+LGY+ K P +P I+GF+LG M E NLRR L +S+GN + +A L +A+ Sbjct: 423 FGLLGYVFVKAGMPAAPFIIGFILGPMAETNLRRGLMLSDGNFVAFLGNPIAATFLGLAL 482 Query: 481 MVIV 484 ++ Sbjct: 483 AFVL 486 Lambda K H 0.326 0.141 0.414 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 838 Number of extensions: 46 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 504 Length of database: 506 Length adjustment: 34 Effective length of query: 470 Effective length of database: 472 Effective search space: 221840 Effective search space used: 221840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory