Align TRAP transporter (characterized, see rationale)
to candidate WP_011383333.1 AMB_RS04540 C4-dicarboxylate ABC transporter
Query= uniprot:A8LI82 (743 letters) >NCBI__GCF_000009985.1:WP_011383333.1 Length = 687 Score = 331 bits (849), Expect = 7e-95 Identities = 212/628 (33%), Positives = 324/628 (51%), Gaps = 62/628 (9%) Query: 155 LFGLPLIVATAGGIVLSWFHKRARSGFSAPDLVLAICGVAVATYLITIY-----GTLMRN 209 L LP+ G ++L F A G P V + ++++++Y G L++ Sbjct: 50 LSSLPVRSIHVGFLLLMVFALYAAMGRGNPVKVATAWALGGLSFILSLYHLIYEGELVQR 109 Query: 210 STGTPFAPIGISIAAVAGTALIMELTRRVAGMALIVIAGIFLAYVFVGQYLPGFLNAPAV 269 S + + VA L+ E RR+ G AL + +F+AY G+ LP L Sbjct: 110 SGDPSTTDLVVGTVMVA---LVFEAARRLMGWALPALCLVFVAYAAFGEILPAPLGHRGY 166 Query: 270 TWQRFFSQVYTDA-GILGPTTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFAAAGQSRG 328 + + +Q + GI G VS+TYI LFI+F +FL+ + + F + A G ++G Sbjct: 167 GFDQIINQYFLGTEGIFGIPCYVSATYIFLFILFGSFLEQAGMIRLFTDVALGTVGHTKG 226 Query: 329 GPAKVAIFASGLMGMINGTSAGNVVATGSLTIPLMKKVGYHKKTAGAVEAAASTGGQIMP 388 GPAKVA+ SGLMG ING+ NVV TG+LTIPLMK+ GY + AGAVEA AS GGQIMP Sbjct: 227 GPAKVAVVTSGLMGTINGSGIANVVTTGALTIPLMKRFGYRSEFAGAVEATASMGGQIMP 286 Query: 389 PIMGAGAFIMAEITGIPYTEIALAAIIPAILYFVSVYFMVDLEAAKLGMRGMSRDELPKF 448 P+MGA AFIMAE I Y E+ AA IPA+LY+ S +MV LEA G+ GM +D+ P Sbjct: 287 PVMGAVAFIMAETLNISYAEVCKAAAIPALLYYASAIWMVHLEAGIAGLHGMPKDQCPSA 346 Query: 449 -NKMVRQVYLFLPIIILIYALFMGYSVIRAGTLATVAAAVVSWFTPFR------------ 495 + RQ YL +P+ L+Y L G++ + +GT+ A+V + Sbjct: 347 QGALRRQWYLMVPLAALVYLLLAGFTPMFSGTVGLALTAIVILGSSIAANIGGMAGRVVF 406 Query: 496 MGPRSIAKA--FEIAGTMSVQIIAV----------------------------------- 518 G IA + F++ + V +AV Sbjct: 407 WGVLGIASSAFFKLGINVVVVTVAVLVGVNFFVRGGRETMRMTVRGLVEGARSAVPVGVA 466 Query: 519 CACAGIIVGVISLTGVGARFSAVLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAA 578 C G I+G ++LTG+ F+ L+ ++ S L L M +++LGMG+PT Y + + Sbjct: 467 CTLVGTIIGTMTLTGIAGSFTQGLVSMSGGSLFLTLILTMIASLILGMGIPTIPTYIITS 526 Query: 579 SVVAPGLVQLGIPLLTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIG 638 S+VAP L ++G+PL+ +H +VFYF +L+ +TPPV LA++AAA I+ +N T + ++ Sbjct: 527 SLVAPMLFKMGVPLVVSHMYVFYFGILADLTPPVGLAAFAAASIARSNFFVTGWWAVRVA 586 Query: 639 IAAFIVPFMFFYNSAILM-DGTWFEVLRAGATAVVGVFFLSSGVQGWFMGGRAAWFLRVG 697 +A F+VPFM Y+ +++M G+ F+ A++ + + G+ W R Sbjct: 587 MAGFVVPFMAVYDPSLMMVSGSLFDTAYVVIKALLAIGLWGAATIGYLWAPMKMW-ERAV 645 Query: 698 LVFAALMLIEGGIMSDLIGVGTAVAIFL 725 V AA +L+ ++D IG + A+FL Sbjct: 646 AVLAAFLLVAAVPLTDEIGFALS-AVFL 672 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: 1336 Number of extensions: 85 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: 687 Length adjustment: 39 Effective length of query: 704 Effective length of database: 648 Effective search space: 456192 Effective search space used: 456192 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 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