Align D-lactate transporter, permease component 2 (characterized)
to candidate 3609311 Dshi_2696 inner-membrane translocator (RefSeq)
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__Dino:3609311 Length = 554 Score = 152 bits (384), Expect = 2e-41 Identities = 99/326 (30%), Positives = 162/326 (49%), Gaps = 41/326 (12%) Query: 11 GLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDETQKD 70 GL GS L A+GL + FG +GV+N AHG L MIGA+ VQ ++ SF Sbjct: 265 GLSLGSVLLLAAIGLAITFGVMGVINMAHGELVMIGAYTTFFVQEIIRTSF--------- 315 Query: 71 FLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHFYKRP 130 P+ + DW++ +A A + VG +ERG ++ Y RP Sbjct: 316 ----------PH------------LFDWSLLIAAPLAFAVAGAVGVAIERGCVRFLYGRP 353 Query: 131 HADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVWRVVYF 190 + +L T+G++++LQ+ V+ +G N + P ++G +G M I Y R+ Sbjct: 354 -LETLLATWGISLILQQTVRSIFGPNNREVGNPSWMSGAFEVGQ---MTITYN--RLWIL 407 Query: 191 FFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAGLAGV 250 FA+ + + L+ T G+ +RA +R +GI + FG+ A +AGLAGV Sbjct: 408 LFALAVFAVLLFVLKKTAIGLQMRAVTQNRAMAANMGIRTGWVDAMTFGLGAGIAGLAGV 467 Query: 251 MYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEIKSLIPG 310 + I++ + ++G ++V SF+VVV GG G++ G + A F LG+ F + + Sbjct: 468 ALSQIDNVSPNLGQSYIVDSFMVVVFGGAGNIWGTLAAAFSLGIANKF--LEPYAGAV-- 523 Query: 311 IDQIIIYVVAIIILLTRPRGLMGRKG 336 + +I++ V I+ + RPRGL KG Sbjct: 524 LAKILVLVFIILFIQKRPRGLFAVKG 549 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: 395 Number of extensions: 17 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 340 Length of database: 554 Length adjustment: 32 Effective length of query: 308 Effective length of database: 522 Effective search space: 160776 Effective search space used: 160776 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: 51 (24.3 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