Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_000182725.1:WP_008510542.1 Length = 333 Score = 332 bits (851), Expect = 9e-96 Identities = 178/359 (49%), Positives = 232/359 (64%), Gaps = 28/359 (7%) Query: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 M S+ L+ + K Y + + I+L++ DGEF++FVGPSGCGKSTLLR IAGLED+++G + Sbjct: 1 MGSLQLKSVHKRYGAQEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAGQV 60 Query: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120 LI+ + V PP R + MVFQSYALYPH+TV NM GLK A K EI+ RV + + Sbjct: 61 LINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKASAM 120 Query: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180 L L+ L R+P +LSGGQRQRVAIGR +VR P++FLFDEPLSNLDA LRVQ R+EIA+LH Sbjct: 121 LALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAKLH 180 Query: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240 + +++TMIYVTHDQVEAMTLAD+IVVLNAG I Q+G P+ LY+ P N FVAGF+GSPQMN Sbjct: 181 RELKATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQMN 240 Query: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHG 300 F+E I A+ T+GIRPEH + E+ T+ G Sbjct: 241 FIEAARIGATGAR--------------------------TIGIRPEHLSVSRESG-TWKG 273 Query: 301 QITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGEA 359 ++ AE LG +LY+ E ++T + G E + + K H F E G+A Sbjct: 274 KVIHAEHLGADTILYVETE-TAGLVTARLFGEQHYNEDDVIFLTPEEGKTHYFDEAGKA 331 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: 361 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 371 Length of database: 333 Length adjustment: 29 Effective length of query: 342 Effective length of database: 304 Effective search space: 103968 Effective search space used: 103968 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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