Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Koxy:BWI76_RS03270 Length = 376 Score = 300 bits (768), Expect = 4e-86 Identities = 176/363 (48%), Positives = 224/363 (61%), Gaps = 9/363 (2%) Query: 1 MADLKLTGVEKAYGD-VKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59 MA + L +EK Y + K + I+L+I GE +VFVGPSGC KST LRMIAGLE I+GG Sbjct: 1 MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60 Query: 60 LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119 + I VND+PP RGIAMVFQ+YALYPH TV +NM+F LK+ K+ + EI VE AAE Sbjct: 61 IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 KL++ + L R PK +SGGQRQRVA+GR+IVR P V+LFDEPLSNLDA LRV+ R++IAQL Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180 Query: 180 KEAMPE----STMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235 ++ E +TM+YVTHDQ EA+TL RI VL G I QV +P +LY P N+FVA FI Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240 Query: 236 GSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMG---AAVNVGVRPEDMVEAA 292 GSP +NL+ I + VE+ G + + L G V G+RPE + A+ Sbjct: 241 GSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHISLAS 300 Query: 293 PGGDY-VFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKV 351 D FEG + + E +G LYF E Q I+ G+ R A Sbjct: 301 DDDDLNTFEGVLTVVENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLRFNLNTAFC 360 Query: 352 HVF 354 HVF Sbjct: 361 HVF 363 Lambda K H 0.316 0.135 0.379 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: 396 Number of extensions: 16 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: 373 Length of database: 376 Length adjustment: 30 Effective length of query: 343 Effective length of database: 346 Effective search space: 118678 Effective search space used: 118678 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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