Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 391 bits (1004), Expect = e-113 Identities = 210/359 (58%), Positives = 256/359 (71%), Gaps = 5/359 (1%) Query: 1 MASVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60 MA VTLR +RK++ EV+ ++L++ADGEFV FVGPSGCGKSTL+R+IAGLE+ SGGDL Sbjct: 1 MAGVTLRGVRKSFGRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDL 60 Query: 61 TIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120 +I G RVND PA RGIAMVFQSYALYPHMT YDNMAFGL L+ T K I VR AA++ Sbjct: 61 SIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARL 120 Query: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180 L I+ LLDRKP+ LSGGQRQRVAIGRAI R+P+VFLFDEPLSNLDA LRV+MRLE A+L Sbjct: 121 LQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLK 180 Query: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240 +L+ TMIYVTHDQVEAMTLAD+IVVL+AG +EQ G+P LYH P NRFVAGFIGSP MN Sbjct: 181 ADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAMN 240 Query: 241 FMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGISAR 300 F++ V + +T V V G +AV+ AA G +T+G+RPEH+ + G+ A Sbjct: 241 FLDVVSEGLTDGSVRVWLPGGVPLDIAVDGAAPAAGTPLTLGVRPEHVGLADGGAGLLAT 300 Query: 301 TMAVESLGDAAYLYAESSVAPDG--LIARIPPLERHTKGETQKLGATPEHCHLFDSAGK 357 +AVE LG + +A DG L+ R+ GE +L E HLF G+ Sbjct: 301 ILAVERLGGETHCHA---ALEDGQRLLVRLDGDRPVAAGERLRLNLRGETAHLFGPDGQ 356 Lambda K H 0.320 0.135 0.384 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: 450 Number of extensions: 18 Number of successful extensions: 1 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: 369 Length of database: 358 Length adjustment: 29 Effective length of query: 340 Effective length of database: 329 Effective search space: 111860 Effective search space used: 111860 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