Align D-lactate transporter, permease component 2 (characterized)
to candidate GFF556 PS417_02830 urea ABC transporter permease
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__WCS417:GFF556 Length = 500 Score = 147 bits (372), Expect = 4e-40 Identities = 105/341 (30%), Positives = 171/341 (50%), Gaps = 48/341 (14%) Query: 4 ILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFET 63 IL Q +G+ GS L ALGL + FG LGV+N AHG + M+GA+ VQ ++ Sbjct: 204 ILGQAFSGMSLGSILLLAALGLAITFGLLGVINMAHGEMLMLGAYSTYMVQLLMQRYMPQ 263 Query: 64 VDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLI 123 E F P + A+P+A + +G +ER +I Sbjct: 264 AIE--------------------FYPLI-------ALPVAFF----VTAAIGMALERTVI 292 Query: 124 KHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYP 183 +H Y RP + +L T+G++++L ++V+ +GA ++ P+ L+G V + ++V P Sbjct: 293 RHLYGRP-LETLLATWGISLMLIQLVRLVFGAQNVEVSNPEWLSGGVQ----VLPNLVLP 347 Query: 184 VWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAA 243 R+V FA+ ++ + L T G+ VRA +R G+ R + FG+ + Sbjct: 348 YNRIVIIAFALCVVVLTWLLLNKTRLGLNVRAVTQNRNMAACCGVPTGRVDMLAFGLGSG 407 Query: 244 VAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNE 303 +AGL GV + I + +G +++ SF+VVV+GG+G L G+V+A F LG+ Sbjct: 408 IAGLGGVALSQIGNVGPDLGQSYIIDSFLVVVLGGVGQLAGSVMAAFGLGIAN------- 460 Query: 304 IKSLIPGIDQII--IYVVAIIILL--TRPRGLMGRKGVMED 340 K L P I ++ I ++A+IIL RP+GL KG + D Sbjct: 461 -KILEPQIGAVLGKILILALIILFIQKRPQGLFALKGRVID 500 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: 350 Number of extensions: 20 Number of successful extensions: 5 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: 500 Length adjustment: 31 Effective length of query: 309 Effective length of database: 469 Effective search space: 144921 Effective search space used: 144921 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: 50 (23.9 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