Align TRAP transporter (characterized, see rationale)
to candidate WP_086511837.1 BZY95_RS20990 C4-dicarboxylate ABC transporter permease
Query= uniprot:A8LI82 (743 letters) >NCBI__GCF_002151265.1:WP_086511837.1 Length = 720 Score = 796 bits (2055), Expect = 0.0 Identities = 431/730 (59%), Positives = 523/730 (71%), Gaps = 27/730 (3%) Query: 4 QTKTADDHLIAEGVDEEPTESNRRLFEGRNFILISTFAALYAAFHMAALNGLSISEWTGI 63 Q + A + EGV + P N R+ G + L+ A H+ ALN Sbjct: 6 QPEQAASKIGTEGVADIPIAHNERVLSGLLGQTVFAACVLFTAMHLYALN---------- 55 Query: 64 EVPFLPTFPMETWNFRIVHIAGALALGFLLFAARTDFPGPGKETPLLGYVAYGLMVPALF 123 P+ETW FRI+H+AG LA+GF + AA T PG+ +G V + M+PA+ Sbjct: 56 ------VSPIETWAFRIIHVAGGLAVGFAITAAYTLDRSPGERH--IGKVEWLAMIPAVA 107 Query: 124 SLGMAASFSMEIASGVMWNGIDEGIKFNETWLF---GLPLIVATAGGIVLSWFHKRARSG 180 ++ AA A G W + W+ L +AT ++ SW + + Sbjct: 108 AIVYAA-----FAIGYAWFIRETQGTPPAGWVLVHMSWALTIATGIAMISSWIWRGSSRS 162 Query: 181 FSAPDLVLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISIAAVAGTALIMELTRRVAG 240 D VL + + VA YL+ + R + GTPFA + + G ALIMELTRRVAG Sbjct: 163 VHWADAVLIVASIIVAAYLLFVLQR-WRMAAGTPFAGQTEFLVSAIGVALIMELTRRVAG 221 Query: 241 MALIVIAGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQVYTDAGILGPTTAVSSTYIILFI 300 +ALIVI +FL Y F G YLPG L + QRFF+ +YTD GILG TTAVSSTYIILFI Sbjct: 222 LALIVITAVFLVYAFAGPYLPGLLEHRGYSPQRFFTYLYTDNGILGATTAVSSTYIILFI 281 Query: 301 IFAAFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTI 360 FAAFLQAS+VGDYFVNFAFAAAG++RGGPAKVA+FASGLMGMINGTSAGNVVATGSLTI Sbjct: 282 TFAAFLQASRVGDYFVNFAFAAAGRARGGPAKVAVFASGLMGMINGTSAGNVVATGSLTI 341 Query: 361 PLMKKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILY 420 PLMKKVGYH ++AG +EAAASTGGQI+PPIMGAGAFIMAEITGIPYTEIA+AA+IPA LY Sbjct: 342 PLMKKVGYHPRSAGGIEAAASTGGQIVPPIMGAGAFIMAEITGIPYTEIAIAALIPAALY 401 Query: 421 FVSVYFMVDLEAAKLGMRGMSRDELPKFNKMVRQVYLFLPIIILIYALFMGYSVIRAGTL 480 F+S+Y MVDLEA + GM+G+ +D+LP F MV+QVYLFLPIIILI LFMGYSVIRAGTL Sbjct: 402 FLSIYLMVDLEARRGGMQGLPKDQLPVFRSMVKQVYLFLPIIILIGTLFMGYSVIRAGTL 461 Query: 481 ATVAAAVVSWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARFSA 540 A V+AAVVSWFTP MGP+++ A + M++ +IAVCACAGIIVGVI+LTGVGARF++ Sbjct: 462 AMVSAAVVSWFTPHWMGPKALLNALSLGARMAIPLIAVCACAGIIVGVIALTGVGARFAS 521 Query: 541 VLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLGIPLLTAHFFVF 600 +LLGIAD S LLALFFAMCI+ILLGMGMPTTAAYAVAASVVAPGL Q+GIP L AHFFVF Sbjct: 522 MLLGIADASHLLALFFAMCISILLGMGMPTTAAYAVAASVVAPGLQQIGIPPLVAHFFVF 581 Query: 601 YFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILMDGTW 660 Y+AVLSAITPPVALA YAAA ISG +P++T++TSFK G+AAFIVPFMFFY+ A+LMDGTW Sbjct: 582 YYAVLSAITPPVALAGYAAAAISGTDPLKTAMTSFKFGLAAFIVPFMFFYSPALLMDGTW 641 Query: 661 FEVLRAGATAVVGVFFLSSGVQGWFMGGRAAWFLRVGLVFAALMLIEGGIMSDLIGVGTA 720 ++LR TA VG++ L++ VQGWF+ G RV L+ AAL +I GG M+DL+GVG Sbjct: 642 MQILRVALTAGVGIYLLAASVQGWFLNGGVNLVQRVLLLAAALSMIAGGWMTDLLGVGIG 701 Query: 721 VAIFLIQKLA 730 +F+ Q A Sbjct: 702 GLVFVWQAAA 711 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: 1657 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: 720 Length adjustment: 40 Effective length of query: 703 Effective length of database: 680 Effective search space: 478040 Effective search space used: 478040 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