Align D-lactate transporter, permease component 2 (characterized)
to candidate PfGW456L13_4608 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4608 Length = 307 Score = 123 bits (308), Expect = 7e-33 Identities = 97/338 (28%), Positives = 158/338 (46%), Gaps = 50/338 (14%) Query: 7 QILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCA-VTVQRVLSLSFETVD 65 Q++NGL GS YALIA+G T+++G +G++NFAHG ++MIG++ A + + + L ++V Sbjct: 10 QLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMLGLDSV- 68 Query: 66 ETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKH 125 PL + A L I + GY +ER + Sbjct: 69 ---------PLLMTA----------------------AFLATIVVTSAYGYSIERIAYRP 97 Query: 126 FYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVW 185 ++ G++I LQ V + P+ + G G +++ Sbjct: 98 LRGSNRLIPLISAIGMSIFLQNTV--LLAQDSKDKSIPNLIPGNFAFGPGGAHEVLISYM 155 Query: 186 RVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVA 245 ++V F +V + G+ F+ + G RA D + LLGIN + + F I AA+A Sbjct: 156 QIVVFVVTLVAMLGLTLFISRSRLGRACRACAEDIKMANLLGINTNNIIALTFVIGAALA 215 Query: 246 GLAGVM----YTPINSPNYHMGMDFLV--LSFVVVVVGGMGSLPGAVLAGFLLGVLESFA 299 +A V+ Y IN PN FLV +F V+GG+GS+PGA+L G +LGV E+F Sbjct: 216 AIAAVLLSMQYGVIN-PN----AGFLVGLKAFTAAVLGGIGSIPGAMLGGLVLGVAEAFG 270 Query: 300 SMNEIKSLIPGIDQIIIYVVAIIILLTRPRGLMGRKGV 337 + ++ + + +++LL RP GL+GR V Sbjct: 271 A----DIFGDQYKDVVAFGLLVLVLLFRPTGLLGRPEV 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: 290 Number of extensions: 18 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