Align D-lactate transporter, permease component 2 (characterized)
to candidate BWI76_RS15335 BWI76_RS15335 branched-chain amino acid ABC transporter permease
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__Koxy:BWI76_RS15335 Length = 524 Score = 143 bits (360), Expect = 1e-38 Identities = 101/339 (29%), Positives = 167/339 (49%), Gaps = 44/339 (12%) Query: 4 ILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFET 63 +L Q GL GS L ALGL + +G LGV+N AHG + MIGA+ VQ+ L+ Sbjct: 228 LLGQAFMGLSLGSVLLLAALGLAITYGLLGVINMAHGEMLMIGAYSCWLVQQALA----- 282 Query: 64 VDETQKDFLGNPLKVKTPYVESW--FGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERG 121 W F P + A+P+A L I G+G +ER Sbjct: 283 -----------------QLAPQWLAFYPLI-------ALPVAFL----ITGGIGMALERT 314 Query: 122 LIKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIV 181 +I+H Y RP + +L T+G++++L ++V+ +GA ++ P L+G V + +++ Sbjct: 315 VIRHLYGRP-LETLLATWGISLMLIQLVRMLFGAQNVEVANPAWLSGGVQ----VLPNLI 369 Query: 182 YPVWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIA 241 P R+ F ++++ + L T GM VRA +R G+ R + FG+ Sbjct: 370 LPWNRLAVLAFVLLVLLFTWLTLNKTRLGMNVRAVTQNRAMAACCGVPTGRVDMLAFGLG 429 Query: 242 AAVAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASM 301 + +AGL GV + + + +G +++ SF+VVV+GG+G L G+V A F LG+ Sbjct: 430 SGIAGLGGVALSQLGNVGPELGQGYIIDSFLVVVLGGVGQLAGSVAAAFGLGIFNKILE- 488 Query: 302 NEIKSLIPGIDQIIIYVVAIIILLTRPRGLMGRKGVMED 340 + + +I+I V+ I+ + RP+GL KG + D Sbjct: 489 ---PQMGAVLGKILILVLIILFIQKRPQGLFALKGRVID 524 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: 364 Number of extensions: 19 Number of successful extensions: 5 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: 524 Length adjustment: 32 Effective length of query: 308 Effective length of database: 492 Effective search space: 151536 Effective search space used: 151536 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