Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 363 bits (931), Expect = e-105 Identities = 187/359 (52%), Positives = 252/359 (70%), Gaps = 8/359 (2%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTI 60 MA ++++++ K + +++ I+L++ D EF+V VGPSGCGKSTLLR+IAGLE ++ G Sbjct: 1 MARIELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDF 60 Query: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARI 120 E+DG+ + +V P RD+AMVFQ+YALYPHM V +NM F++++ E +V+ AA Sbjct: 61 EIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAET 120 Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLH 180 L L +++R PK LSGGQRQRVA+GRAI+R+P+ FLFDEPLSNLDAALRV+MRLE+ RLH Sbjct: 121 LGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLH 180 Query: 181 KELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMG 240 K+L ATMIYVTHDQVEA+T+AD++VVLNGG I+QVGSPL+LY +PAN FVA F+G+P M Sbjct: 181 KQLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMN 240 Query: 241 FLKGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHLELAKPGDCALQV 300 L G + A + L L H +AV LGIRPEHL++ +PG+ L Sbjct: 241 IL-------PVSGAASGVMATNGMMLTLDHMH-DTAAAVELGIRPEHLDVVEPGEGHLIA 292 Query: 301 TADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDADGVAL 359 ADV ERLGSDT + + L +R G++ R GE L L + AQ+ H+FD G+AL Sbjct: 293 VADVVERLGSDTNIYAKVDGLGPLMVRKHGNVPVRSGERLGLRVQAQNAHIFDDRGIAL 351 Lambda K H 0.320 0.137 0.389 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: 389 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: 355 Length adjustment: 29 Effective length of query: 338 Effective length of database: 326 Effective search space: 110188 Effective search space used: 110188 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