Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= reanno::BFirm:BPHYT_RS16095 (369 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 321 bits (822), Expect = 2e-92 Identities = 182/367 (49%), Positives = 238/367 (64%), Gaps = 17/367 (4%) Query: 1 MASVTLRNIRKAYDEN-EVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGD 59 MA+V+LR I K Y+ + + I+L+I DGEF+VFVGPSGC KST +RMIAGLEDISGG+ Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 60 LTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAK 119 + I +VND+ P RGIAMVFQ+YALYPH T++DNMAFGLK+ K EI V +AA+ Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 120 ILHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARL 179 L I LL RKPK++SGGQRQRVA+GRAI RKP VFLFDEPLSNLDA LRV MR++ A+L Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 180 HDELK-----TTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFI 234 H LK TMIYVTHDQ EA+TL D+I VL+ GN+ QV +PT LY+ P N+FVA FI Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 235 GSPKMNFMEGVVQSVTHDGVTVRYETGETQRVAVEPAAVKQG---DKVTVGIRPEHLHVG 291 GSP +N ++ ++ ++ + V G + + +G V GIRPEH+ + Sbjct: 241 GSPSINLIDTAIRK-NNERLYVEIAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHISLA 299 Query: 292 MAEDGIS---ARTMAVESLGDAAYLYAESSVAPDGLIARI--PPLERHTKGETQKLGATP 346 +D ++ VE++G +LY V LIAR+ + G+T + Sbjct: 300 SDDDDLNTFEGVLTVVENMGSEKFLY--FIVGGKELIARVDTQDINPFHIGKTLRFNLNT 357 Query: 347 EHCHLFD 353 CH+FD Sbjct: 358 AFCHVFD 364 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: 400 Number of extensions: 21 Number of successful extensions: 3 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: 376 Length adjustment: 30 Effective length of query: 339 Effective length of database: 346 Effective search space: 117294 Effective search space used: 117294 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