Align Tricarboxylic transport TctA (characterized, see rationale)
to candidate WP_011842050.1 RSPH17029_RS15390 tripartite tricarboxylate transporter permease
Query= uniprot:E4PJQ9 (508 letters) >NCBI__GCF_000015985.1:WP_011842050.1 Length = 498 Score = 313 bits (801), Expect = 1e-89 Identities = 188/506 (37%), Positives = 270/506 (53%), Gaps = 14/506 (2%) Query: 1 METLGFLMDGFAVALTPYNLMFALFGAFVGTLIGCLPGLGPANGVAILIPLAFTLGLPPE 60 METL +L+ F P L G G +IG LPGL GVA+LIPL F G+ P Sbjct: 1 METLSYLLPLFE----PATLGAIALGTLGGLIIGALPGLTATMGVALLIPLTF--GMSPV 54 Query: 61 TAMILLTAVYAGAMYGGRISSILLNIPGDEPAMMTCLDGYPMAQKGRAADALAVSAIASF 120 + +L +Y G +YGG +S+ILL PG + T LDGYPMA +G A AL ++ IAS Sbjct: 55 MGLNMLIGIYIGGIYGGCVSAILLRTPGTPSSAATVLDGYPMALRGEAGKALGLATIAST 114 Query: 121 AGGLIGTIGLIMLAPVLAKFALTFGPAEYFALFLLAFATLGGITGKNPVKTVVAATLGIM 180 GGL + L LAP LA AL FG AEYFAL + ++G + +K V+A LGI+ Sbjct: 115 LGGLFAAVVLATLAPQLAGIALKFGAAEYFALAFFGLTIIASLSG-DILKGVIAGMLGIL 173 Query: 181 ISTVGIDISTGTQRYTFGVLELYEGIDFILAIVGLFAISELLFFVESR-MGRGRDKMNVG 239 IS VG D TG RYTFGV G F A++GLFA+SE+ +E G G VG Sbjct: 174 ISCVGADPITGMLRYTFGVSGFASGFAFTPALIGLFALSEVFTQLERLGAGDGAQVQKVG 233 Query: 240 KLTLTMKELVMTIPTQLRGGVLGFISGVLPGAGASLGSFISYTLEKQVVGKKGKFGEGDI 299 +L + +RG ++G + G++PG G+ S+I+Y ++ KFG G Sbjct: 234 GRWPAWADLRESRGALVRGSIIGTLIGIVPGTGSGTASWIAYNEARRASKTPEKFGTGHA 293 Query: 300 RGVVAPEAGNNGASSGALVPMLTLGVPGSGTTAVLLAMLISLNITPGPLMFTQNADIVWG 359 G+ A E+ NN + AL+P+L LGVPG TAVL+ L+ + PGP++F N D+V G Sbjct: 294 PGICATESANNAVCAAALIPLLALGVPGDVVTAVLMGGLMIQGLAPGPMLFQTNPDVVVG 353 Query: 360 VIAALLIGNVLLLVLNIPLVGFFVKLLSVPPMYLLPIVTMVAFVGIYSISHSTFDLYFMV 419 + + + + + + L+ F ++L +P L + + F+G Y+I+ + DLY MV Sbjct: 354 IFGGTFLATIFMFLFGMALIPVFSRILMIPRHILAVAIIVFCFIGAYAINLNPVDLYTMV 413 Query: 420 AFGVAGYFLRKLEIPLVPIILGLLLGPEMEKNLGHALVLSDGEWSVLWASPLAMGLWIVA 479 FGV G+ + K + + L+LGP +E NL L+ + + + P+ + Sbjct: 414 GFGVLGWGMHKFGFSQAALCIALILGPMLESNLRRGLLQAGDDLVTFLSGPITL-----L 468 Query: 480 GLGLILPYLVGPLLRRRMNAAMKESP 505 LGL L L+ P + R AA K SP Sbjct: 469 FLGLSLLSLLWPWIAAR-RAAGKPSP 493 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: 836 Number of extensions: 56 Number of successful extensions: 6 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: 498 Length adjustment: 34 Effective length of query: 474 Effective length of database: 464 Effective search space: 219936 Effective search space used: 219936 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 Apr 10 2024. 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