Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__BFirm:BPHYT_RS04435 Length = 646 Score = 217 bits (553), Expect = 4e-61 Identities = 109/251 (43%), Positives = 170/251 (67%), Gaps = 1/251 (0%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 +L+++ + F GL A+ DV L + G + GLIGPNG+GK+T+ N+LTG+Y P+ GT+ Sbjct: 391 ILQLRGILMQFSGLKALNDVDLTVQRGTIHGLIGPNGSGKSTMMNVLTGIYVPTAGTLEY 450 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 G L GK+ +IA G+ RTFQN++LF ++T L+NVL+ + ++ L + Sbjct: 451 RGASLAGKTSAQIALSGIARTFQNVQLFGEMTALENVLVGLHHTFNANLADVGLMSSRYR 510 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 + E+ + +A +L+ LD A A+NL YG+QR LEI RALA +P++L LDEPAAG+ Sbjct: 511 REERAARERAFGMLRFVGLDNVAAEEARNLPYGKQRLLEIARALALDPQLLLLDEPAAGL 570 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242 + EL +IR+++D IT++LIEH M++VM V +R+ VL++G+ IA+G P +I++N Sbjct: 571 TAPDIKELVAIIRKVRDH-GITVVLIEHHMDVVMSVCDRVSVLDFGQKIAEGKPADIQSN 629 Query: 243 KRVIEAYLGGE 253 ++VIEAYLGG+ Sbjct: 630 EKVIEAYLGGQ 640 Lambda K H 0.319 0.139 0.385 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: 352 Number of extensions: 16 Number of successful extensions: 2 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: 254 Length of database: 646 Length adjustment: 31 Effective length of query: 223 Effective length of database: 615 Effective search space: 137145 Effective search space used: 137145 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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