Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__BFirm:BPHYT_RS17470 Length = 362 Score = 209 bits (531), Expect = 1e-58 Identities = 121/339 (35%), Positives = 194/339 (57%), Gaps = 12/339 (3%) Query: 22 YALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERN 81 + L + ++ DG ++GPSGCGK+T+L +++GL S G + G+ V + P++RN Sbjct: 18 FVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEGSISIAGKVVNQLEPKDRN 77 Query: 82 IAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAA 141 IA VFQ +Y M+VAEN+ + L+ V QI +RV A++LE+ L ++ L+ Sbjct: 78 IAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAAQILELEALLQRKPRELSG 137 Query: 142 DAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQV 201 +Q++++GR +VR + A LFDEPL+ +D L+ Q+R +++++H L T +YVTHDQ+ Sbjct: 138 GQRQRVAMGRAIVR-EPAVFLFDEPLSNLDARLRVQMRLEIQRLHARLATTSLYVTHDQI 196 Query: 202 EALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAH--RDGENLSV 259 EA+T A +V+VM +G A Q+G+ ++ERPA FV FIGSPGMN L DG V Sbjct: 197 EAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVASFIGSPGMNLLEGRVSDDGAFFEV 256 Query: 260 AGHRLASP------VGRALPAG-ALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQM 312 AG+ P +GR + G +GIRPE+++ Q A TV + +G + Sbjct: 257 AGNGPKLPLTDVASIGREVARGREWTLGIRPEHMSPGQADAPHATL-TVDSCELLGADNL 315 Query: 313 LTAKVGEHTVKARFTPETRLPSSGDTAWLQVLGEHTCYY 351 + G+H V R P P++G+ + + H ++ Sbjct: 316 AHGRWGKHDVTVRL-PHAHRPAAGEALQVALPARHLHFF 353 Lambda K H 0.320 0.136 0.395 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: 304 Number of extensions: 17 Number of successful extensions: 2 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: 358 Length of database: 362 Length adjustment: 29 Effective length of query: 329 Effective length of database: 333 Effective search space: 109557 Effective search space used: 109557 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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