Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate WP_080518270.1 DHAF_RS10320 transporter
Query= uniprot:E4PJQ9 (508 letters) >NCBI__GCF_000021925.1:WP_080518270.1 Length = 500 Score = 462 bits (1188), Expect = e-134 Identities = 228/503 (45%), Positives = 341/503 (67%), Gaps = 14/503 (2%) Query: 1 METLGFLMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPE 60 +E + L+ GF +AL+ N+M L G VG +IG LPG GPA GVAIL+P+ F G+PP Sbjct: 4 LENISNLLMGFQLALSFTNIMVCLLGIVVGVIIGALPGFGPAAGVAILLPMTF--GMPPS 61 Query: 61 TAMILLTAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASF 120 TAMI+L +Y GAM+GG IS+IL+N PGD A+MT LDGYP+AQ+G+A AL +S IASF Sbjct: 62 TAMIMLCGIYFGAMFGGAISAILINTPGDSAAVMTSLDGYPLAQQGKAGPALGMSTIASF 121 Query: 121 AGGLIGTIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIM 180 GG +G I L ++AP++AKFA++FGP EYF L +L TL G+TGK+ K + A LG+ Sbjct: 122 IGGTVGVIALTLIAPIIAKFAVSFGPPEYFGLMVLGLTTLAGMTGKDATKGFMMALLGLF 181 Query: 181 ISTVGIDISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVESRMGRGRDKMNVGK 240 +S +G DI TG QR+ FG+ L+ GIDFI ++GLF +SE+L E + K+ + K Sbjct: 182 LSVIGADIMTGQQRFVFGIPSLWVGIDFIPVVMGLFGLSEVLINCEEDI-----KITMQK 236 Query: 241 LTLTMKELVMT-------IPTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGK 293 + LT++ ++ + + RG +LGF GVLPGAGA++ SFISY+ K++ K Sbjct: 237 MKLTLRNILPSKQDMKDSVGALSRGSILGFFIGVLPGAGATIASFISYSTAKKISKHPEK 296 Query: 294 FGEGDIRGVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQN 353 FG+G I GV APE+ NN A+SGA+VP+LTLG+PGSGTTAV+L L+ L + PGPL+F N Sbjct: 297 FGKGAIEGVAAPESANNAAASGAMVPLLTLGLPGSGTTAVMLGALLMLGLNPGPLLFRDN 356 Query: 354 ADIVWGVIAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTF 413 + V+ +IA+L N++L++LN+ + F +L VP L+P + + +G+YS+ + Sbjct: 357 PEFVFTIIASLYFANIMLVILNLVGIPAFTSVLKVPYSILMPCIVIFLILGVYSLEFTMI 416 Query: 414 DLYFMVAFGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAM 473 +++ M+ FG+ GYF++K++ P P++L L+LGP E++L +L LS G++ V + SP++ Sbjct: 417 NVWIMIFFGIVGYFMKKMDYPGAPLVLALVLGPITEQSLRRSLALSHGDFGVFFTSPISC 476 Query: 474 GLWIVAGLGLILPYLVGPLLRRR 496 L I++ L +I P + G ++++ Sbjct: 477 TLIIISILVVIWPLIKGRCIKKK 499 Lambda K H 0.325 0.144 0.425 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: 829 Number of extensions: 59 Number of successful extensions: 5 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: 508 Length of database: 500 Length adjustment: 34 Effective length of query: 474 Effective length of database: 466 Effective search space: 220884 Effective search space used: 220884 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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