Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate SM_b20972 SM_b20972 sugar uptake ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2490 (367 letters) >FitnessBrowser__Smeli:SM_b20972 Length = 391 Score = 392 bits (1008), Expect = e-114 Identities = 207/368 (56%), Positives = 264/368 (71%), Gaps = 8/368 (2%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 MA ++I NL+K F I++GIDLE+ D EFV F+GPSGCGKSTLLR IAGLE + G+I Sbjct: 1 MATIRIDNLRKSFGSHEILRGIDLEIADGEFVCFLGPSGCGKSTLLRSIAGLENLDGGSI 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120 L RDIT++ A+RD+AMVFQ YALYPHM+VRKN+SF L L G+ + ++ +V+ AA I Sbjct: 61 RLGDRDITDLPSARRDIAMVFQNYALYPHMNVRKNLSFGLALNGMKRNEIDRRVNNAAEI 120 Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L + LL+RKP+QLSGGQRQRVAIGRAIVR PK+FL DEPLSNLDA LRV MR+ELA LH Sbjct: 121 LRITELLDRKPRQLSGGQRQRVAIGRAIVREPKLFLLDEPLSNLDAGLRVTMRVELAALH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 + L TMIYVTHDQVEAMTL+D+VVVL+ GR+ Q G+PLEL+++PANLFVAGF+G+P+M Sbjct: 181 ERLGVTMIYVTHDQVEAMTLSDRVVVLDKGRVSQFGTPLELFYRPANLFVAGFIGSPRMN 240 Query: 241 FLKGKVTRVESQSCEVQLDAGTLINLPL-----SGATLSVGSAVTLGIRPEHLEIASPGQ 295 FL V E + V L AG ++ P+ S +L+ VTLGIRP+ LE+ SP + Sbjct: 241 FLPAGV--AEQAATRVTL-AGGGLSRPVTLDTRSSESLNRDRPVTLGIRPDKLELTSPEE 297 Query: 296 TTLTVTADVGERLGSDTFCHVITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTD 355 L T + ERLG+++ H+ G LT +RG + +HL L P HCHLFD + Sbjct: 298 AHLAGTVRLVERLGTESHVHIRVEGGGDLTAVVRGTHPVASRDQVHLRLPPEHCHLFDAE 357 Query: 356 GVAVARPL 363 G A+AR L Sbjct: 358 GTAIARRL 365 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: 443 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: 391 Length adjustment: 30 Effective length of query: 337 Effective length of database: 361 Effective search space: 121657 Effective search space used: 121657 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