Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2490 (367 letters) >FitnessBrowser__HerbieS:HSERO_RS02210 Length = 372 Score = 397 bits (1020), Expect = e-115 Identities = 203/362 (56%), Positives = 260/362 (71%), Gaps = 2/362 (0%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 MA + I+NL K ++ +++ I+LE+ D EFVVFVGPSGCGKSTLLR+IAGLEE+S+G + Sbjct: 1 MAAVSIRNLAKRYDDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGDL 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120 ++ R + EV +KR +AMVFQ+YALYPHMS+ NM+F L +AG K +++ V AA+I Sbjct: 61 DIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAAKI 120 Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L + LL+RKP+ LSGGQRQRVAIGRAI R P +FLFDEPLSNLDAALRV+MRLE A+LH Sbjct: 121 LHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKLH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 +L+ TMIYVTHDQ+EAMTLADK+VVL+ GRIEQVGSP +LYH PAN FVAGF+G+PKM Sbjct: 181 DDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKMN 240 Query: 241 FLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTLTV 300 F+ G V +++ +VQL G L + G+TL VG VTLG+RPEHL IA GQ L Sbjct: 241 FIDGTVAAIQADGVQVQLPGGGLQWAAVDGSTLQVGQKVTLGVRPEHLNIAQ-GQAALQA 299 Query: 301 TADVGERLGSDTFCHVITANGE-PLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAV 359 E LG ++ + E L +R+ + + +G L L DPA CHLF DG A+ Sbjct: 300 RCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADPARCHLFGADGQAL 359 Query: 360 AR 361 R Sbjct: 360 PR 361 Lambda K H 0.319 0.136 0.384 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: 391 Number of extensions: 12 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: 367 Length of database: 372 Length adjustment: 30 Effective length of query: 337 Effective length of database: 342 Effective search space: 115254 Effective search space used: 115254 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: 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