Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__WCS417:GFF5028 Length = 370 Score = 234 bits (596), Expect = 4e-66 Identities = 135/302 (44%), Positives = 183/302 (60%), Gaps = 10/302 (3%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 + R V K+Y G +K++ L I++GEFL L+GPSG GK+T + +AG ET T G I Sbjct: 11 VSFRGVQKSYD-GENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQ 69 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 + + ++ + P RDI MVFQ+YAL+P M+V EN+ F L +R + + DI V RV ++ Sbjct: 70 LAGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISERVKRVLSMV 129 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 Q++ R P QLSGGQQQRVA+ RAL P++ L DEPL LD +LR M+ E+K +HQ Sbjct: 130 QLDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQ 189 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 RL T VYVTHDQ EA+T+ D+VAV G IQQ P+ +Y P N FVA+FIG N Sbjct: 190 RLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVANFIGE--NNR 247 Query: 244 VPLRLQRKDG-RLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSAS 302 + RL G R V L G+ LA+N + G V L +RPE++ L G S S Sbjct: 248 LNGRLHSHSGERCVVELARGEKVEALAVNVGQVG---GPVTLSVRPERVSL---NGSSES 301 Query: 303 SI 304 + Sbjct: 302 CV 303 Lambda K H 0.318 0.135 0.382 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: 353 Number of extensions: 13 Number of successful extensions: 1 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: 386 Length of database: 370 Length adjustment: 30 Effective length of query: 356 Effective length of database: 340 Effective search space: 121040 Effective search space used: 121040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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