Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate Pf1N1B4_3377 Tricarboxylate transport membrane protein TctA
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3377 Length = 509 Score = 364 bits (935), Expect = e-105 Identities = 192/505 (38%), Positives = 309/505 (61%), Gaps = 19/505 (3%) Query: 7 LSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAESALILL 66 L QG + +TP ++ + +IG +G +VG+LPGLG NGVA+LLPL F + SA+ILL Sbjct: 7 LLQGMNLILTPGHIGLMVIGVLLGILVGVLPGLGAPNGVALLLPLTFTMS--PVSAIILL 64 Query: 67 ATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSFFGSLIA 126 + +Y G +GG I+SIL N+PG+ +++ T DGYPMA++G+ AL+ + S+ G+L Sbjct: 65 SCMYWGALFGGSITSILFNIPGEPSSVATTFDGYPMAREGRAAEALTAAFSSALIGALAG 124 Query: 127 IGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLGLATVGV 186 + + + +A ++++F E+FA+ + A M PLK+ +A +IG +A VG+ Sbjct: 125 VLLLTFLSTKIAAFAMSFSSPEFFAVYLLAFCTFIGMSKNPPLKTVVAMMIGFAMAAVGM 184 Query: 187 DANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLE--------HTSSGQTMVRKT 238 D +G R TFD L G+ F V VIGLF + EIL +E H ++ +T Sbjct: 185 DTVSGNLRLTFDQPILMTGISFEVAVIGLFGIGEILCTVEEGLVFRGEHARITPMIILRT 244 Query: 239 GRMLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGD 298 L + T +RS+++G ++G+ PG G T AS ++Y ++ S N ++FGKG+ Sbjct: 245 WAKL------PRYWWTIVRSTLVGCWMGITPG-GPTAASFMSYSLARRFSKNRENFGKGE 297 Query: 299 IRGVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVW 358 + GV APE A++A+ + +PMLTLG+PGS T AVM+G L ++ + PGP +F EQ D VW Sbjct: 298 LEGVIAPETADHAAGTSALLPMLTLGIPGSATAAVMLGGLMIWGLHPGPTLFVEQHDFVW 357 Query: 359 GLIAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLM 418 GLIA++ + NV+ LI+ + + LF +L IP + P I V A+G Y+VH++ FD+VLM Sbjct: 358 GLIASMYLGNVVSLIVVLATVPLFASILRIPFSIIAPIIIMVCAIGAYSVHNSFFDVVLM 417 Query: 419 VALGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIM 478 + G LGY+ +K+ +P++PL+L VLG+ E R+++ S+G++ I W + + L Sbjct: 418 LGFGALGYLFKKLGYPIAPLVLAAVLGDKAEDAFRQSMLFSDGHIGIFWSNPLVGGLTTT 477 Query: 479 AIMVIVVPPVLRLLRK--HSRKPQV 501 A++++ P + ++L+ RKP V Sbjct: 478 ALLMLFWPLISKVLQTLLGLRKPHV 502 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: 758 Number of extensions: 39 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: 509 Length adjustment: 34 Effective length of query: 470 Effective length of database: 475 Effective search space: 223250 Effective search space used: 223250 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 17 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