Align D-lactate transporter, permease component 2 (characterized)
to candidate BPHYT_RS00695 BPHYT_RS00695 branched-chain amino acid ABC transporter permease
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS00695 Length = 291 Score = 131 bits (330), Expect = 2e-35 Identities = 93/325 (28%), Positives = 153/325 (47%), Gaps = 50/325 (15%) Query: 8 ILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDET 67 ILN L S L+ALGL ++FG + +VN AH IGA+ Q V Sbjct: 4 ILNILGYVSILILVALGLAIVFGMMDIVNLAHAEWVTIGAYALAVAQAV----------- 52 Query: 68 QKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHFY 127 GG W LA+ A + +G+ +ER +I+ Y Sbjct: 53 ------------------------GGQQAFW---LALFAAPAVGAFLGWCLERFIIRLLY 85 Query: 128 KRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVWRV 187 RP D +L T+ ++++LQ+V++ +G P+ AP + V GS YP +R+ Sbjct: 86 DRP-LDTLLATYAISLILQKVLELIFGTQPMLVYAPFSGAVPVPGGS-------YPAYRI 137 Query: 188 VYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAGL 247 A+ + G + T FG +RA + GI+ R I F AA+A L Sbjct: 138 FVIGVALTVTAGCWLLFARTRFGTQLRAVIQHPAMAEAAGIDTRRLNRIAFCGGAALASL 197 Query: 248 AGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEIKSL 307 AGV+ P+ S H+G+ +L +F V+V+GG+GS+ G++L ++G E+ S + Sbjct: 198 AGVLVAPMVSVESHLGVSYLAKAFFVIVLGGIGSIAGSILGSAVIGTAETLLSYR----I 253 Query: 308 IPGIDQIIIYVVAIIILLTRPRGLM 332 P + ++ V++I+++ RP+GL+ Sbjct: 254 DPSLASAVVLVLSIVVIRFRPQGLI 278 Lambda K H 0.329 0.147 0.439 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: 235 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 340 Length of database: 291 Length adjustment: 27 Effective length of query: 313 Effective length of database: 264 Effective search space: 82632 Effective search space used: 82632 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 (21.8 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