Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_072906038.1 BUB13_RS04630 C4-dicarboxylate ABC transporter permease
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_900142125.1:WP_072906038.1 Length = 574 Score = 328 bits (840), Expect = 6e-94 Identities = 180/526 (34%), Positives = 292/526 (55%), Gaps = 15/526 (2%) Query: 163 HQRERSVFSVPDLVLIVCSLAVAAYFLVVYNT-SMRMSTGTSFAPVGISFAAIAGTALIM 221 ++ + + V D +L++ S+ +Y++ + + R T ++ A+ G + + Sbjct: 54 YRSKNVLLRVLDYILMITSIISLSYWVANFEAINYRTGAETELD----TWMAVIGVIISV 109 Query: 222 ELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQV-YTDAGILGPTTAV 280 EL RRV G VIIG + LAY G ++P + G + ++ Y GI G V Sbjct: 110 ELARRVVGNVFVIIGGLMLAYGVYGAHVPDLFAHAGATFPELCIEIFYRSDGIFGIMANV 169 Query: 281 SSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGN 340 +TYI+LF++F AFL+ +F++F AA G GGP KV++ ASGL G I+G++ N Sbjct: 170 LATYILLFVLFGAFLEKCGAQRFFIDFPLAAVGHKIGGPGKVAVVASGLFGSISGSAIAN 229 Query: 341 VVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAI 400 VSTG+ TIP+MKK G+ AG +E AAS GG MPPIMGAG FIMAE+TG PY+ I + Sbjct: 230 TVSTGAFTIPMMKKAGFKPHIAGGIEPAASIGGMFMPPIMGAGGFIMAELTGEPYSRIML 289 Query: 401 AAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQCYLFVPIIILIVALFMG 460 A+ PAI+YF SV+ MV +EA K + G + E + + + Y +P++ + + + G Sbjct: 290 VALFPAIMYFFSVFVMVHYEAKKDNIVG-EKSEHSAMEILKAEWYYTLPLVSITIFMLYG 348 Query: 461 YSVIRAGTLATVSAAVVSWL-SPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVIS 519 YS + L V+ +VSW ++G + L+A + +++I G+I+GV++ Sbjct: 349 YSPGYSAILGLVTCIIVSWFRKDTRIGPKRFLEAAREGAESSLKIGATVGVIGIIIGVLT 408 Query: 520 LTGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGI 579 +G+ F+ +++ +A S +L ++ S++LGMG+P TAAY + A V P L LG+ Sbjct: 409 YSGLVLTFADIVIQMAGGSLILTILLIALASLVLGMGVPVTAAYLITAVVAVPALTHLGV 468 Query: 580 EPLTAHFFVFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFY 639 L AH V++ + S ITPPV +A++A A I+ AN +T+ ++F+ ++ PF+F Y Sbjct: 469 NELAAHMIVYWLSQDSNITPPVCIAAFAGATIAKANMWKTAFSAFKFAKFLYLGPFLFGY 528 Query: 640 NGALLMEAGWFEIARALVTATFGVYMLSGGVLGWFASISASWITRL 685 ++ +I +A G Y S WF +S WI ++ Sbjct: 529 VPGFSLDGSTTDIVKAFALIIIGTYAYS-----WF--LSGIWIQKI 567 Lambda K H 0.327 0.139 0.410 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: 999 Number of extensions: 62 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: 729 Length of database: 574 Length adjustment: 38 Effective length of query: 691 Effective length of database: 536 Effective search space: 370376 Effective search space used: 370376 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: 54 (25.4 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