Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 327 bits (837), Expect = 4e-94 Identities = 167/289 (57%), Positives = 213/289 (73%), Gaps = 4/289 (1%) Query: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 MASV +R + K + T I R +D+DI DGEF V VGPSGCGKSTLLR++AGLE+IT G++ Sbjct: 1 MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60 Query: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120 LI VN++ PKDR + MVFQ+YALYPHMTV +NMAF L LA DK + RV+ A+I Sbjct: 61 LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120 Query: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180 L L++LL+R P+ LSGGQRQRVA+GR +VR+P+VFLFDEPLSNLDA LRVQMR EI LH Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180 Query: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240 QR+++T IYVTHDQ+EAMT+AD+IVV+ G + Q G+PL LY YP N FVAGF+GSP MN Sbjct: 181 QRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMN 240 Query: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAV--SPGDPLTLGIRPEH 287 F+ + + +E G + P G+A+ + G +T G+RPEH Sbjct: 241 FIPA-TLRRNATGAEVEFADGTRVPAPY-GAALQGNDGQKVTYGVRPEH 287 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: 393 Number of extensions: 18 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: 361 Length adjustment: 30 Effective length of query: 341 Effective length of database: 331 Effective search space: 112871 Effective search space used: 112871 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