Align D-lactate transporter, permease component 2 (characterized)
to candidate RR42_RS07535 RR42_RS07535 ABC transporter permease
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__Cup4G11:RR42_RS07535 Length = 288 Score = 167 bits (422), Expect = 4e-46 Identities = 102/329 (31%), Positives = 171/329 (51%), Gaps = 49/329 (14%) Query: 3 AILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFE 62 + +Q LN + G L+A GLTLIFG +GV+N AHG+ +M+GA+ A T+ + Sbjct: 5 SFFIQCLNSIQYGLLLFLVASGLTLIFGIMGVINLAHGSFYMLGAYLAFTLAGL------ 58 Query: 63 TVDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGL 122 G +I AVPL I+ A+ GYV+E Sbjct: 59 ----------------------------TGSLLI--AVPLGIVLAVAF----GYVLEWVF 84 Query: 123 IKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVY 182 + Y+R H Q+L+T+GL +V +E+ + P L+ + +G+ D+ Y Sbjct: 85 FSYLYEREHLQQVLMTYGLILVFEELRSILVDDDVHGVTVPAMLDWALPIGN----DMTY 140 Query: 183 PVWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAA 242 PV+R+ +++ ++ ++ T GM++RAG +RE V LGIN+ + +F + Sbjct: 141 PVYRLFISAICLLVAAAMYLVIRRTRLGMMIRAGATNREMVQSLGINVTVLYRFVFALGV 200 Query: 243 AVAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMN 302 A+A LAG++ P++S MG L++ FVVVV+GG+GS+ GA++A LLG +++F Sbjct: 201 ALAVLAGMIAAPVSSVYPGMGSQVLIVCFVVVVIGGIGSVKGAMVASLLLGFVDTFG--- 257 Query: 303 EIKSLIPGIDQIIIYVVAIIILLTRPRGL 331 K +++Y++ +ILL +P+GL Sbjct: 258 --KVFWQEASGVLVYLLMALILLWKPQGL 284 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: 258 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 2 Length of query: 340 Length of database: 288 Length adjustment: 27 Effective length of query: 313 Effective length of database: 261 Effective search space: 81693 Effective search space used: 81693 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