Align D-lactate transporter, permease component 2 (characterized)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__Miya:8500415 Length = 306 Score = 116 bits (290), Expect = 8e-31 Identities = 104/345 (30%), Positives = 164/345 (47%), Gaps = 58/345 (16%) Query: 1 MDAILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLS 60 M+ + + N L GS YALIALG TL++G L ++NFAHG +FM+GA+ A V +L Sbjct: 1 MEIFIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLL--- 57 Query: 61 FETVDETQKDFLGNPLKV-KTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVME 119 LG+ L V P G A + VPL +L + GVG +E Sbjct: 58 -----------LGDLLGVFNLP----------GWAALALTVPLTML----LTAGVGVTLE 92 Query: 120 RGLIKHFYKR-PHADQILVT-FGLAIVLQEVVKYFYGANPIQTPAPDALNGVV-NLGSII 176 R + ++ H +++T ++L+ GA+ + PD ++ VV GS+ Sbjct: 93 RIAYRPLRRKGAHRLYVVITALMCGLILENGNLALLGAS--RRKLPDMVDKVVYTFGSVS 150 Query: 177 GMDIVYPVWRVVYFFFAVVIIGGIFSFLQF----TTFGMVVRAGMADRETVGLLGINIDR 232 ++ VW ++ F +F LQF T GM +RA D+ + L+GI +D Sbjct: 151 VTNL--KVWVIITAFL-------VFFLLQFIVTRTRIGMAMRAVAWDKFALPLMGIPLDS 201 Query: 233 RFTIMFGIAAAVAGLAGVMYT---PINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAG 289 F + + AGLAG+++ PI P +MG +F+ VVGG+G + GA + G Sbjct: 202 IIVFTFVLGSGFAGLAGLLFAMSYPILDP--YMGAMVGWKAFIAAVVGGIGDIRGAFIGG 259 Query: 290 FLLGVLESFASMNEIKSLIPG-IDQIIIYVVAIIILLTRPRGLMG 333 FLL +E + + +P + + + ++IL RP GL G Sbjct: 260 FLLAFIEIM-----VAAFLPSTFRDLFAFTILLMILWQRPTGLFG 299 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: 224 Number of extensions: 11 Number of successful extensions: 2 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: 340 Length of database: 306 Length adjustment: 28 Effective length of query: 312 Effective length of database: 278 Effective search space: 86736 Effective search space used: 86736 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