Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate WP_086508166.1 BZY95_RS01120 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >NCBI__GCF_002151265.1:WP_086508166.1 Length = 371 Score = 369 bits (948), Expect = e-107 Identities = 192/365 (52%), Positives = 246/365 (67%), Gaps = 1/365 (0%) Query: 1 MAHLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTI 60 M L + + K + G + + IDL + D EFVVFVGPSGCGKSTLLR+IAGLE+++ G + Sbjct: 1 MGRLTLAGIGKDYAGVEVSRDIDLTIEDGEFVVFVGPSGCGKSTLLRMIAGLEDISHGEM 60 Query: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARI 120 LDG I EV P +RD+ MVFQ+YALYPHM+V +NM+F L LA +KAE+ ++V AA + Sbjct: 61 RLDGERINEVPPQERDIGMVFQSYALYPHMTVAENMAFGLKLARTDKAEIRRRVEHAAEM 120 Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L LG +LERKPK+LSGGQRQRVAIGR +V+ P +FLFDEPLSNLDAALRV MR+++A LH Sbjct: 121 LHLGELLERKPKELSGGQRQRVAIGRTLVKEPAVFLFDEPLSNLDAALRVDMRVQIAELH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 + L ATMIYVTHDQVEAMTLAD++V+L GGRI QVG+PL LYH PA L VA F+G+P++ Sbjct: 181 RRLGATMIYVTHDQVEAMTLADRIVLLAGGRIAQVGAPLSLYHFPATLEVARFIGSPRIN 240 Query: 241 FLKGKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLALPGDCTLQV 300 + +V RQ V L G + + + GA L G TL +R E D L Sbjct: 241 VIPVEVLDPGRQRTSVRLPDGATLAVAVDGARLRAGDKATLAVRAEDFVTPADADARLTA 300 Query: 301 TADVSERLGSDTFCHV-LTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDANGVAV 359 V+ERLG +T H+ + E LT R+ G G+ + L L E CHLF A+G A Sbjct: 301 RLMVAERLGYETLAHLRVEGVSETLTQRLDGLTRLEDGQAVELGLSGERCHLFAADGKAC 360 Query: 360 ARPLR 364 R +R Sbjct: 361 PRQVR 365 Lambda K H 0.321 0.137 0.390 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: 410 Number of extensions: 14 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: 371 Length adjustment: 30 Effective length of query: 337 Effective length of database: 341 Effective search space: 114917 Effective search space used: 114917 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 24 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