Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 228 bits (581), Expect = 2e-64 Identities = 126/309 (40%), Positives = 183/309 (59%), Gaps = 4/309 (1%) Query: 6 LRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDGM 65 + + K +D+ + D++L+I GE +G SG GKSTL+RM+AG E + G + +DG Sbjct: 23 IERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLDGQ 82 Query: 66 RVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKILHIDH 125 + D+ P +R I M+FQSYAL+PHMT+ N+AFGLK K EI+ V+ K++H++ Sbjct: 83 DITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHMEP 142 Query: 126 LLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDELKT 185 RKP QLSGGQRQRVA+ R++ ++PK+ L DEP+ LD LR +M+LE + + + Sbjct: 143 YAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDILEAVGV 202 Query: 186 TMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMNFMEGV 245 T + VTHDQ EAMT+A++I +++ G + Q GSP +Y +PANR VA FIGS +N EG Sbjct: 203 TCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGS--VNLFEGD 260 Query: 246 VQSVTHDGVTVRY-ETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGISARTMAV 304 + D V + + V + +V V IRPE H+ E AR Sbjct: 261 IVEDEVDHVVINVANIPQPFYVGYGVSTSVDTTQVWVAIRPEKTHIS-REQPEDARNWCA 319 Query: 305 ESLGDAAYL 313 + D AYL Sbjct: 320 GKVEDIAYL 328 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: 329 Number of extensions: 9 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: 378 Length adjustment: 30 Effective length of query: 339 Effective length of database: 348 Effective search space: 117972 Effective search space used: 117972 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: 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:
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