Align D-lactate transporter, permease component 2 (characterized)
to candidate Ac3H11_3703 Urea ABC transporter, permease protein UrtB
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3703 Length = 527 Score = 150 bits (378), Expect = 9e-41 Identities = 99/331 (29%), Positives = 163/331 (49%), Gaps = 40/331 (12%) Query: 10 NGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDETQK 69 +G+ GS L+ALGL + +G +GV+N AHG L MIGA+ VQ + QK Sbjct: 237 SGISLGSILLLVALGLAITYGLMGVINMAHGELMMIGAYATYVVQGIF----------QK 286 Query: 70 DFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHFYKR 129 F G DW + A+ A VG V+ERG+++ Y R Sbjct: 287 YFPG---------------------AFDWYLVAALPLAFGASAAVGAVLERGVLRFLYGR 325 Query: 130 PHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVWRVVY 189 P + +L T+G+++VL ++V+ +GA + P ++G V + S ++ P R+V Sbjct: 326 P-LETLLATWGISLVLMQLVRTIFGAQNVGVENPAWMSGGVQVLS----NLTLPYNRLVI 380 Query: 190 FFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAGLAG 249 FA+ ++ G+ + T G+ VR +R +G+N R T+ F + + +AGLAG Sbjct: 381 IGFAIAVLLGMGYLIARTRLGLFVRGVTQNRPIASCMGVNTARIDTMAFALGSGIAGLAG 440 Query: 250 VMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEIKSLIP 309 + + + +G ++V +F+VVV+GG+G L G V A LG+L F + + Sbjct: 441 CALSQVGNVGPDLGQSYIVDAFMVVVLGGVGQLAGTVYAALGLGILNKF--LEGWAGAV- 497 Query: 310 GIDQIIIYVVAIIILLTRPRGLMGRKGVMED 340 + +I + V II + RP+G+ KG D Sbjct: 498 -LAKIAVLVFIIIFIQKRPQGIFAVKGRTAD 527 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: 369 Number of extensions: 20 Number of successful extensions: 4 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: 527 Length adjustment: 32 Effective length of query: 308 Effective length of database: 495 Effective search space: 152460 Effective search space used: 152460 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