Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 303 bits (776), Expect = 4e-87 Identities = 166/345 (48%), Positives = 220/345 (63%), Gaps = 13/345 (3%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA +Q I+K FG +KGIDL I GEF+V VGPSGCGKSTLLR +AGLE+ D G++ Sbjct: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 +DG+ I D RD+AMVFQSYALYPHM+V ENM F LKL + I ++V + + Sbjct: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L + L R PKELSGGQRQRVA+GRA+ R V LFDEPLSNLDA LR Q R+EI +LH Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 + +T IYVTHDQ+EA TL DR+ VL+DG+IEQ+GTP E+Y +P N F+A FIG+P+MN Sbjct: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 Query: 241 F-----LEGAVLEKIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDFQIDISENLG 295 L V ++ P A A +G+RP+ + T +G Q+D+ E LG Sbjct: 241 VVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRT----TGATPVGG-QVDLIEALG 295 Query: 296 GQQMLHGTLAGNNVRILVDSMDNFSMK--QTLPLKIDLTKAHLFD 338 + +++ T G + + D ++ + L ID ++AH FD Sbjct: 296 AETLIYVTTPG-GAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFD 339 Lambda K H 0.318 0.136 0.383 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: 315 Number of extensions: 15 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: 347 Length of database: 350 Length adjustment: 29 Effective length of query: 318 Effective length of database: 321 Effective search space: 102078 Effective search space used: 102078 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 (21.7 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