Align TctA, component of The tricarboxylate transporter, TctABC (characterized)
to candidate PP_1416 PP_1416 putative Tricarboxylate transport protein TctA
Query= TCDB::Q9FA44 (504 letters) >FitnessBrowser__Putida:PP_1416 Length = 504 Score = 678 bits (1750), Expect = 0.0 Identities = 327/505 (64%), Positives = 414/505 (81%), Gaps = 3/505 (0%) Query: 1 MDTWIYLSQGFAVAMTPENLVIALIGCFVGTIVGLLPGLGPINGVAILLPLAFALHLPAE 60 MDT YL QGF +A++P NLV AL G +GT+VGLLPGLGPINGVA+L+P+AFAL LP E Sbjct: 1 MDTLSYLGQGFGIALSPYNLVTALSGTLIGTVVGLLPGLGPINGVALLIPIAFALGLPPE 60 Query: 61 SALILLATVYIGCEYGGRISSILLNVPGDAAAIMTALDGYPMAQQGKGGVALSISAVSSF 120 SALILLA VY+GCEYGGRISSILLN+PG+A+ +MT LDGYPMA+QG GVALS+SA SSF Sbjct: 61 SALILLAAVYLGCEYGGRISSILLNIPGEASTVMTTLDGYPMARQGLAGVALSLSAWSSF 120 Query: 121 FGSLIAIGGIILFAPLLAQWSLAFGPAEYFALMVFAIACLGSMMAQNPLKSFLAALIGLG 180 G+ IA G++LFAPLLA+W++AFGPAEYF LMVFAI LG M PLK+F+AALIGL Sbjct: 121 IGAFIATCGMVLFAPLLAKWAIAFGPAEYFVLMVFAIVALGGMAGDKPLKTFIAALIGLF 180 Query: 181 LATVGVDANTGVYRFTFDSVHLSDGVQFIVVVIGLFSVSEILLMLEHTSSGQTMVRKTGR 240 L+ VG+DAN+GVYRFT DSVHL+DG+QF+V+V+GLFS+SEILL+LE T G V+ TGR Sbjct: 181 LSAVGIDANSGVYRFTGDSVHLADGIQFVVLVLGLFSISEILLLLEKTHHGHQAVKATGR 240 Query: 241 MLFNLKEGAQCIGTTLRSSVIGFFVGVLPGAGATIASAITYMTEKKLSGNSDSFGKGDIR 300 MLFN KE A +R ++GF +GVLPGAGAT+ASA+ YMTEK+++G S FGKGD R Sbjct: 241 MLFNFKEAASVFLVNIRCGLLGFIMGVLPGAGATLASAVAYMTEKRMAGESGKFGKGDAR 300 Query: 301 GVAAPEAANNASACGSFIPMLTLGVPGSGTTAVMMGALTLYNITPGPAMFTEQPDIVWGL 360 G+AAPE A AS CG+ +PMLTLGVPGSGTTAVM+GALTLYNITPGP +F +QPDIVWGL Sbjct: 301 GLAAPETAIGASCCGALVPMLTLGVPGSGTTAVMIGALTLYNITPGPLLFEQQPDIVWGL 360 Query: 361 IAALLIANVMLLIMNIPLIGLFTRMLTIPLWFVVPAIAAVSAVGVYAVHSTTFDLVLMVA 420 IA+L +AN+ML+I+NIP+I +FTR+L +P W +VP IA ++A+GVYAVH+TTFDL LMV Sbjct: 361 IASLFVANIMLVILNIPMIRIFTRILAVPNWALVPVIAIITAIGVYAVHATTFDLFLMVG 420 Query: 421 LGVLGYILRKMHFPMSPLILGFVLGEMLEQNLRRALSISNGNMAILWQSGVAKALLIMAI 480 +G++GYI+RK+ FP+SP++LGF+LG ++EQNLRRALSISNG + ILW S ++ + + + Sbjct: 421 IGIMGYIMRKLDFPLSPILLGFILGGLMEQNLRRALSISNGELGILWSSPISMGIWALVV 480 Query: 481 MVIVVPPVLRLLRKHS--RKPQVDA 503 +++ + P+LR+ RK S R+ DA Sbjct: 481 VMLAL-PLLRIWRKRSLQRRALADA 504 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: 941 Number of extensions: 35 Number of successful extensions: 3 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: 504 Length adjustment: 34 Effective length of query: 470 Effective length of database: 470 Effective search space: 220900 Effective search space used: 220900 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