Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate BPHYT_RS35680 BPHYT_RS35680 sugar ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__BFirm:BPHYT_RS35680 Length = 360 Score = 340 bits (871), Expect = 5e-98 Identities = 180/355 (50%), Positives = 232/355 (65%), Gaps = 3/355 (0%) Query: 1 MASVTLRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60 MA+V L I K Y + +V+ I+LDI DGEFVV VGPSGCGKSTLMRM+AGLE+ISGGDL Sbjct: 1 MAAVQLSGIFKRYGDTQVVHGIDLDIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60 Query: 61 TIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120 I G R N +AP +R I+MVFQSYALYPH+++Y+N+AFG ++ + AAK+ Sbjct: 61 MIGGTRANSLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESSASFKPRIEAAAKM 120 Query: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180 L++ LDR P+ LSGGQRQRVA+GRA+ R+P +FLFDEPLSNLDA LRV+MR E LH Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180 Query: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240 LK T+IYVTHDQ+EAMT+AD+IVV++AG +EQ+G P LY PAN FVA F+GSP MN Sbjct: 181 QRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMN 240 Query: 241 FMEGVVQS-VTHDGVTVRYETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGISA 299 F EGV+ S G+ + G + PA+ G KVT+G+RPEH+ + Sbjct: 241 FAEGVIASRAQGQGLALNLTGGGEIVLEGAPASAVVGAKVTLGVRPEHIETMTPTPDATM 300 Query: 300 RTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHTKGETQKLGATPEHCHLFDS 354 VE G +LY + + + R + G+ L EH HLFD+ Sbjct: 301 EVEVVEPTGAETHLYGKIGGSTWCVTTR--QRSKIEPGQRVTLRLPAEHIHLFDT 353 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: 394 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 369 Length of database: 360 Length adjustment: 29 Effective length of query: 340 Effective length of database: 331 Effective search space: 112540 Effective search space used: 112540 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