Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__HerbieS:HSERO_RS01355 Length = 381 Score = 378 bits (970), Expect = e-109 Identities = 198/371 (53%), Positives = 259/371 (69%), Gaps = 10/371 (2%) Query: 1 MASVTLRDICKSY-DGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGD 59 MAS+TLR K+Y D P+ R++DLDI + EF VF+GPSGCGKSTLLR IAGLED+TSGD Sbjct: 1 MASITLRAAQKAYGDAPPVIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGD 60 Query: 60 LLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119 L I +RVND+P RSV MVFQSYAL+PHMTV ENM+FGL LA + K EI+++V A Sbjct: 61 LFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAAR 120 Query: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179 ILQL++LL+RKPK+LSGGQRQRVAIGR +VR P VFLFDEPLSNLDA LR Q RIEIARL Sbjct: 121 ILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARL 180 Query: 180 HQRI-RSTMIYVTHDQVEAMTLADKIVVLNA-------GEIAQVGQPLHLYHYPKNRFVA 231 H++ +++++YVTHDQVEAMTLAD+IV+L+A G IAQVG P+ LYH+P+NRFVA Sbjct: 181 HRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVA 240 Query: 232 GFLGSPQMNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMP 291 GF+GSP+MNF+ + + + L L A+ PG +T+G+RPEH + Sbjct: 241 GFIGSPRMNFLPAQVAGVQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEIG 300 Query: 292 DEADFTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCH 351 + + H ++ + ERLG+ ++L Q ++ G+ R+T GE + + Sbjct: 301 SQGQYGIHREVVLVERLGEQTYVHLDEPAGQPLVAKAA-GDARITRGERVRVAIAPACAY 359 Query: 352 LFRENGEACTR 362 LF ++G A TR Sbjct: 360 LFDQDGLALTR 370 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: 408 Number of extensions: 20 Number of successful extensions: 5 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: 381 Length adjustment: 30 Effective length of query: 341 Effective length of database: 351 Effective search space: 119691 Effective search space used: 119691 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: 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