Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 345 bits (885), Expect = 1e-99 Identities = 187/364 (51%), Positives = 243/364 (66%), Gaps = 12/364 (3%) Query: 1 MASVTLRDICKSYD-GTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGD 59 MA+V+LR I K Y+ G IDL+I DGEF+VFVGPSGC KST LR+IAGLEDI+ G+ Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 60 LLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119 + I N++VNDLPPKDR + MVFQ+YALYPH TV +NMAFGLK+ K EIKRRVE AE Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179 L++ +LL RKPK++SGGQRQRVA+GR +VR+P VFLFDEPLSNLDA LRV MR++IA+L Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 180 HQRIR-----STMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFL 234 H+ ++ +TMIYVTHDQ EA+TL D+I VLN G I QV P LY+YP N+FVA F+ Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 235 GSPQMNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPG---DPLTLGIRPEHFVMP 291 GSP +N ++ AI + E + +E+ G + +P + G P+ GIRPEH + Sbjct: 241 GSPSINLIDT-AIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHISLA 299 Query: 292 DEAD--FTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADK 349 + D TF G +TV E +G LY + + + + G+T L Sbjct: 300 SDDDDLNTFEGVLTVVENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLRFNLNTAF 359 Query: 350 CHLF 353 CH+F Sbjct: 360 CHVF 363 Lambda K H 0.322 0.139 0.405 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: 416 Number of extensions: 16 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: 371 Length of database: 376 Length adjustment: 30 Effective length of query: 341 Effective length of database: 346 Effective search space: 117986 Effective search space used: 117986 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 (21.9 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