Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 306 bits (783), Expect = 8e-88 Identities = 170/351 (48%), Positives = 228/351 (64%), Gaps = 14/351 (3%) Query: 1 MASVTLRDICKSYDGTP--ITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSG 58 M+ + LR I K+Y G + ID+DI GEF++ VGPSGCGKSTL+ IAGLE IT G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 59 DLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVA 118 +++D + ++ + PKDR + MVFQSYALYP M+V EN+AFGLK+ + K EI + VE VA Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 119 EILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIAR 178 ++LQ+ L+ +KP +LSGGQ+QRVA+GR + R P+++LFDEPLSNLDA LRV+MR EI + Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 179 LHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238 LHQR+++T++YVTHDQ+EAMTLAD+I VL GE+ Q+G P +Y P+N FVAGF+GSP Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 239 MNFVEVRAISASPE-TVTIELPSGYPLTLPV-DGSAVSPGDPLTLGIRPEHFVMP----D 292 M+FV V + G + LPV + A G + LGIRPEH P + Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300 Query: 293 EADFTFHGQIT--VAERLGQYNLLYLTLERLQDVITLC-VDGNLRVTEGET 340 + G+ T V E G + L +L D C +D VT GET Sbjct: 301 DQTLVAKGEFTIEVTEPTGPD---VIALIQLNDTNVHCRIDPEHPVTWGET 348 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: 442 Number of extensions: 21 Number of successful extensions: 2 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: 372 Length adjustment: 30 Effective length of query: 341 Effective length of database: 342 Effective search space: 116622 Effective search space used: 116622 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 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