Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 333 bits (854), Expect = 4e-96 Identities = 183/366 (50%), Positives = 241/366 (65%), Gaps = 14/366 (3%) Query: 1 MTGLLLKDIRKSY-GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59 M + L+ I K Y +HGIDL+I +GEF+VFVGPSGC KST LRMIAGLE+I+GG+ Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 60 MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119 ++I +VND+PP RGIAMVFQ+YALYPH TV+DNMAFG+++ + K+EI RRV AA+ Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179 L++T L R PK +SGGQRQRVA+GRAI R P VFLFDEPLSNLDA LRV+ R++IA+L Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 180 SERMSD----TTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFI 235 + + TMIYVTHDQ EA+TL DRI VL+ G+I QV P +LY P N FVA FI Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 236 GSPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENG---KTASFGVRPEDLRVTE 292 GSP++N+I I ++ V +A G + + G K FG+RPE + + Sbjct: 241 GSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHISLAS 300 Query: 293 ADDFL--FEGTVSIVEALGEVTLLYIEGLVENEPIIAKM--PGIARVGRGDKVRFTADKA 348 DD L FEG +++VE +G LY +V + +IA++ I G +RF + A Sbjct: 301 DDDDLNTFEGVLTVVENMGSEKFLYF--IVGGKELIARVDTQDINPFHIGKTLRFNLNTA 358 Query: 349 KLHLFD 354 H+FD Sbjct: 359 FCHVFD 364 Lambda K H 0.320 0.137 0.387 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: 398 Number of extensions: 19 Number of successful extensions: 4 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: 362 Length of database: 376 Length adjustment: 30 Effective length of query: 332 Effective length of database: 346 Effective search space: 114872 Effective search space used: 114872 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