Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__BFirm:BPHYT_RS17470 Length = 362 Score = 301 bits (771), Expect = 2e-86 Identities = 166/357 (46%), Positives = 224/357 (62%), Gaps = 24/357 (6%) Query: 1 MAGIKIDKINKFYGTTQ-ALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGR 59 MA + + + K Y Q L I++D+ DGEFVV VGPSGCGKSTLLR +AGLE +S G Sbjct: 1 MAALTLQGVKKTYDGKQFVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEGS 60 Query: 60 IEIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119 I I G+ V +EP DR++AMVFQ+YALYPHM+V ENM + +K+ G + +R+ AA+ Sbjct: 61 ISIAGKVVNQLEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAAQ 120 Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179 +L+LE L RKP +LSGGQRQRVA+GRAIV+ P+VFLFDEPLSNLDA+LRVQMR+E++ L Sbjct: 121 ILELEALLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180 Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAM 239 H +L T +YVTHDQ+EAMT+A +++V+N+G EQ+G+P ++Y +P + FVA FIGSP M Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVASFIGSPGM 240 Query: 240 NVFSSDVG----------------LQDI-SLDASAA-----FVGCRPEHIEIVPDGDGHI 277 N+ V L D+ S+ A +G RPEH+ H Sbjct: 241 NLLEGRVSDDGAFFEVAGNGPKLPLTDVASIGREVARGREWTLGIRPEHMSPGQADAPHA 300 Query: 278 AATVHVKERLGGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEA 334 TV E LG ++L + G G + R+ G A+ + LH FD A Sbjct: 301 TLTVDSCELLGADNLAH-GRWGKHDVTVRLPHAHRPAAGEALQVALPARHLHFFDPA 356 Lambda K H 0.320 0.139 0.396 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: 349 Number of extensions: 14 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: 338 Length of database: 362 Length adjustment: 29 Effective length of query: 309 Effective length of database: 333 Effective search space: 102897 Effective search space used: 102897 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