Align D-lactate transporter, permease component 2 (characterized)
to candidate Pf6N2E2_3579 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3579 Length = 304 Score = 144 bits (362), Expect = 4e-39 Identities = 103/341 (30%), Positives = 167/341 (48%), Gaps = 50/341 (14%) Query: 1 MDAILLQ-ILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSL 59 MD I LQ ++NGL GS Y LIA+G T+++G +G++NFAHG ++MI A+ A +L+ Sbjct: 1 MDGIFLQQLINGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAISLALLA- 59 Query: 60 SFETVDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAIL----FAIPIMIGVG 115 +FG E + PL IL F + + G Sbjct: 60 --------------------------YFGIE--------SFPLMILGTLVFTVVVTGVYG 85 Query: 116 YVMERGLIKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSI 175 +V+ER K ++ G++++LQ + GA Q P L G + L Sbjct: 86 WVIERVAYKPLRNSTRLAPLISAIGISLILQNYAQISQGAR--QQGVPTLLEGAMRLD-- 141 Query: 176 IGMDIVYPVWRVVYFFFAVVIIGGIFSFL-QFTTFGMVVRAGMADRETVGLLGINIDRRF 234 IG V + ++ A + +++ ++T G + RA DR+ +LGIN DR Sbjct: 142 IGSGFVQLTYTKIFILIAAFAGMAVLTYIIKYTKLGRMCRATQQDRKMASILGINTDRVI 201 Query: 235 TIMFGIAAAVAGLAGVMYT-PINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLG 293 + +F I AA+A LAGV+ T + +++ G + +F V+GG+GSLPGA+L G +LG Sbjct: 202 SYVFIIGAAMAALAGVLITMNYGTFDFYAGFIIGIKAFTAAVLGGIGSLPGAMLGGIILG 261 Query: 294 VLESFASMNEIKSLIPGIDQIIIYVVAIIILLTRPRGLMGR 334 + ES S + + + + ++IL+ RP+GL+GR Sbjct: 262 ISESLFS----GLINSDYKDVFSFSLLVLILIFRPQGLLGR 298 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: 256 Number of extensions: 13 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: 304 Length adjustment: 28 Effective length of query: 312 Effective length of database: 276 Effective search space: 86112 Effective search space used: 86112 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