Align ABC transporter (characterized, see rationale)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__HerbieS:HSERO_RS01355 Length = 381 Score = 340 bits (871), Expect = 5e-98 Identities = 185/353 (52%), Positives = 245/353 (69%), Gaps = 12/353 (3%) Query: 18 ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDLEPRERGV 77 ++R+V L+I EF VF+GPSGCGKSTLLR IAGL+ + GDL I G+RVND+ +R V Sbjct: 19 VIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGDLFIGGKRVNDVPSAQRSV 78 Query: 78 GMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQLDKLLQRKPKELSGG 137 MVFQSYAL+PHM+VY+N+SFGL LAK K + ++V + A+ILQL++LLQRKPKELSGG Sbjct: 79 AMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAARILQLEELLQRKPKELSGG 138 Query: 138 QRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRL-GSTMIYVTHDQVE 196 QRQRVA+GRA+ R P + LFDEPLSNLDA+LR Q R EIARLH + ++++YVTHDQVE Sbjct: 139 QRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARLHRQFEQASVVYVTHDQVE 198 Query: 197 AMTLADKIVVLNG-------GRVEQVGSPRELYERPASRFVAGFLGSPRMNFLSARLQTP 249 AMTLAD+IV+L+ G + QVG+P ELY P +RFVAGF+GSPRMNFL A++ Sbjct: 199 AMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVAGFIGSPRMNFLPAQVAGV 258 Query: 250 GETSLVDTLVWG-ITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGV--VVTAVEYL 306 E ++ L T L L G +++G+RPEH+ + + G G+ V VE L Sbjct: 259 QENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEI-GSQGQYGIHREVVLVERL 317 Query: 307 GSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVALSR 359 G +TYVHL+ +PL+ + A G+RV + + +LFD DG+AL+R Sbjct: 318 GEQTYVHLDEPAGQPLVAKAAGDARITRGERVRVAIAPACAYLFDQDGLALTR 370 Lambda K H 0.320 0.137 0.394 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: 378 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: 381 Length of database: 381 Length adjustment: 30 Effective length of query: 351 Effective length of database: 351 Effective search space: 123201 Effective search space used: 123201 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 (21.8 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