Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate H281DRAFT_00093 H281DRAFT_00093 amino acid/amide ABC transporter membrane protein 1, HAAT family
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >lcl|FitnessBrowser__Burk376:H281DRAFT_00093 H281DRAFT_00093 amino acid/amide ABC transporter membrane protein 1, HAAT family Length = 551 Score = 141 bits (355), Expect = 4e-38 Identities = 96/292 (32%), Positives = 155/292 (53%), Gaps = 15/292 (5%) Query: 8 LINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALIT---FLAIGSLGITW 64 L GLSLG++ L A+G + YG+IG+IN AHGE MIGA+ + F G W Sbjct: 258 LFAGLSLGSVLLLAALGLAITYGLIGVINMAHGEFLMIGAYATYVVQNLFQRFAPGGFDW 317 Query: 65 VPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGA 124 P LV + AS + A+ G +ER+ + L P L L++ G+S+ L ++L GA Sbjct: 318 YP---LVAVPASFVAAALVGIVIERLVLKHLYGRP-LETLLTTFGISLILIQATRMLFGA 373 Query: 125 RSKPLQPILP----GNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRAC 180 ++ +Q + P G +T+M + + Y RLA + ++ ++ ++T+T LG RA Sbjct: 374 QN--VQVVNPSWMSGGVTVMANLI-LPYNRLAILAFSLIVVGIAWAVLTKTRLGLFVRAV 430 Query: 181 EQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAV 240 Q+++MA +GV RV S F GA +A + G + I G + +G + +F A V Sbjct: 431 TQNRRMAACVGVKTARVDSYAFAFGAGIAGLGGCALSQI-GNVGPDLGQSYIIDSFMAVV 489 Query: 241 LGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGL 292 LGG+G L G ++GG +GL+ + G+ +A ++VL + RP G+ Sbjct: 490 LGGVGQLAGTVIGGFGLGLVSKAIEPFWGAVLAKIAVLVLIVLFIQKRPQGM 541 Lambda K H 0.329 0.144 0.425 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: 405 Number of extensions: 30 Number of successful extensions: 3 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: 301 Length of database: 551 Length adjustment: 31 Effective length of query: 270 Effective length of database: 520 Effective search space: 140400 Effective search space used: 140400 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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