Align TRAP transporter (characterized, see rationale)
to candidate WP_011159000.1 TX73_RS17650 C4-dicarboxylate ABC transporter
Query= uniprot:A8LI82 (743 letters) >NCBI__GCF_000195775.1:WP_011159000.1 Length = 688 Score = 312 bits (800), Expect = 3e-89 Identities = 189/540 (35%), Positives = 297/540 (55%), Gaps = 27/540 (5%) Query: 195 VATYLITIYGTLMRNST-------GTPF--APIGISIAAVAGTALIMELTRRVAGMALIV 245 VA +++TI L+ ST G F AP + IA + AL+ME RR G +L++ Sbjct: 107 VALFVLTIGAALVLMSTIRKAAEAGWEFGGAPTHVFIAGLVMWALLMEALRRTGGWSLLL 166 Query: 246 IAGIFLAY-VFVGQYLPGFLNAPAVTWQRFFS-QVYTDAGILGPTTAVSSTYIILFIIFA 303 F Y +F G G L T ++ + V + +LG + +I F++F Sbjct: 167 CIFPFTVYPLFAGARWLGPLGGSQSTLEQATAYHVLSGESLLGIPIQAFADTVIGFLVFG 226 Query: 304 AFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPLM 363 L + G +F+N +F+ G RGG AKV IFAS L+GM++G+ NV+ G++TIP+M Sbjct: 227 TALMLTGAGKFFINLSFSICGTFRGGAAKVCIFASALLGMMSGSIISNVLTAGTMTIPVM 286 Query: 364 KKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFVS 423 KK G+ A A+EA ASTG + PP+MGA AF++A+ + Y E+ALAAI+PA LY++ Sbjct: 287 KKSGFRASYAAAIEACASTGAVLAPPVMGATAFVIAQFLNVSYAEVALAAIVPAALYYIG 346 Query: 424 VYFMVDLEAAKLGMRGMSRDELPKFNKMVRQVYLF-----LPIIILIYALFMGYSVIRAG 478 ++ VD AA+ G+ G+ R ELP + +++ + + L +++L+Y ++ A Sbjct: 347 LFMQVDAYAARHGLEGIPRSELPSLWQTLKEGWYYAFVIALLVVMLLYFKRESHAPFYAT 406 Query: 479 TLATVAAAVVSWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARF 538 L V + S T + +G SI + E+ G V++I + A G+++G S+TGV + Sbjct: 407 ALLLVLNQIFSKETRWTLG--SIVRFLEVNGRTFVELIGILAGCGLLIGAFSMTGVISSL 464 Query: 539 SAVLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLGIPLLTAHFF 598 +A LL +A + L L +++LG+G+ TTA Y A +VAP L +LG+ + H F Sbjct: 465 AADLLRLAGDNAFLLLAMCAITSLILGLGLTTTACYIFLAILVAPALEKLGLNRMAVHMF 524 Query: 599 VFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMDG 658 +FY+ +LS+ITPPVA+AS+AAAGI+G+ M+T S +G + +PF F N A+++ G Sbjct: 525 IFYWGMLSSITPPVAIASFAAAGIAGSPAMKTGWESMWVGSIIYFIPFFFVMNPALVLQG 584 Query: 659 --TWFEVLRAGATAVVGVFFLSSGVQGWFMG-------GRAAWFLRVGLVFAALMLIEGG 709 + L A G + G+QG+ +G G W LRV LV +L G Sbjct: 585 PDPYLAALGLLTLAAAGTLCICGGIQGYQVGIGNLRHAGALEWPLRVALVIGGFVLATPG 644 Lambda K H 0.327 0.140 0.419 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: 1282 Number of extensions: 87 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: 743 Length of database: 688 Length adjustment: 39 Effective length of query: 704 Effective length of database: 649 Effective search space: 456896 Effective search space used: 456896 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 (21.7 bits) S2: 55 (25.8 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