Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate H281DRAFT_02378 H281DRAFT_02378 amino acid/amide ABC transporter membrane protein 1, HAAT family
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__Burk376:H281DRAFT_02378 Length = 294 Score = 139 bits (350), Expect = 8e-38 Identities = 96/317 (30%), Positives = 167/317 (52%), Gaps = 39/317 (12%) Query: 1 MDIF-------IQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAM---VG 50 MDIF + Q++ GLV GS YA+++LG +++G+LN+INFAHG + M+GAM +G Sbjct: 1 MDIFGIPLPAMLSQLLLGLVNGSFYAILSLGLAVIFGLLNVINFAHGALFMLGAMLAWMG 60 Query: 51 LSLLKVVQQVAPGLPGIVQLVIA--IVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITA 108 S G+P LV+A IVG V IER R L L L+ Sbjct: 61 FSYF--------GVPYWAMLVLAPLIVGLFGVA------IERSMLRWLYKLDHLYGLLLT 106 Query: 109 IGVSILLQTLAMMIWGRSPLPF--PQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVL 166 G++++++ + I+G S P+ P + S ++ + + ++ +++ Sbjct: 107 FGLTLVVEGVFRSIYGSSGQPYDVPSAL-SGATNLGFMFLPNYRAWVVVASLIVCFATWF 165 Query: 167 IVEKTKMGRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFA 226 ++EKT++G +RA ENP++ G++ +I +T+ G LAA AGV+ AA Sbjct: 166 VIEKTRLGAYLRAGTENPKLVEAFGINVPLMITLTYGFGVALAAFAGVL-AAPVIQVSPL 224 Query: 227 MGFVPGLKAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAF 286 MG + F+ V+GG+G+I G++L G++LG+IE L + + + + F Sbjct: 225 MGQPMIITVFAVVVIGGMGSIMGSILTGLMLGVIEGLTRVFYPEASATVV---------F 275 Query: 287 IVLIIVLTLRPSGIMGE 303 +++ +VL +RP+G+ G+ Sbjct: 276 VIMALVLLVRPAGLFGK 292 Lambda K H 0.328 0.144 0.416 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: 262 Number of extensions: 16 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: 309 Length of database: 294 Length adjustment: 27 Effective length of query: 282 Effective length of database: 267 Effective search space: 75294 Effective search space used: 75294 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: 48 (23.1 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