Align D-lactate transporter, permease component 2 (characterized)
to candidate GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__Marino:GFF3113 Length = 307 Score = 132 bits (333), Expect = 9e-36 Identities = 99/334 (29%), Positives = 161/334 (48%), Gaps = 42/334 (12%) Query: 7 QILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDE 66 Q++NGL GS YALIA+G T+++G +G++NFAHG ++MIGA+ A+ L+ Sbjct: 10 QLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGLAA------- 62 Query: 67 TQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHF 126 +G A + + +A+L A+ + +G+ +ER + Sbjct: 63 ------------------------LGIAWLPLILIVALLCAMIVSSSMGWAVERVAYRPV 98 Query: 127 YKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVWR 186 R ++ G++I LQ V G+ I PA ++G N GS G + + Sbjct: 99 RGRHRLIPLISAIGMSIFLQNYVHLAQGSRNIGFPA--LIDGGFNFGSGDGFQMSLSYMQ 156 Query: 187 VVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAG 246 + F ++ + + F+ + G RA D LLGI+ +R + F I AA+A Sbjct: 157 ITIFITTLICMTALSLFISRSRTGRACRAVSQDLGMANLLGIDTNRIISATFVIGAALAA 216 Query: 247 LAGV---MYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNE 303 +AG+ MY P + G + +F V+GG+GS+PGA+L G +LGV ES S Sbjct: 217 VAGLLLGMYYGSVDPLF--GFIAGLKAFTAAVLGGIGSIPGAMLGGLILGVAESMTS--- 271 Query: 304 IKSLIPGIDQIIIYVVAIIILLTRPRGLMGRKGV 337 L +I + + I+ILL +P GL+G+ V Sbjct: 272 -GYLSGEYKDVISFSLLILILLFKPTGLLGKPEV 304 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: 243 Number of extensions: 16 Number of successful extensions: 2 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: 307 Length adjustment: 28 Effective length of query: 312 Effective length of database: 279 Effective search space: 87048 Effective search space used: 87048 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