Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 232 bits (591), Expect = 1e-65 Identities = 128/291 (43%), Positives = 180/291 (61%), Gaps = 7/291 (2%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 + R + K+Y G ++++ L I+ GEFL L+GPSG GK+T + +AG ET T G I+ Sbjct: 11 VSFRGIQKSYD-GESLIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIL 69 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 + + ++ + P RD+ MVFQ+YAL+P M+V EN+ F L +R M + DI V R ++ Sbjct: 70 LDGRAINNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMV 129 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 Q+E NR P QLSGGQQQRVA+ RAL P++ L DEPL LD +LR +M+ E+K +H+ Sbjct: 130 QLEGFRNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHE 189 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 RL T VYVTHDQ EA+T+ D+VAV G IQQ P+ +Y P N FVA+F+G N Sbjct: 190 RLGVTVVYVTHDQGEALTMSDRVAVFHQGQIQQIEDPRTLYEKPVNTFVANFLGE--NNR 247 Query: 244 VPLR-LQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIML 293 +P L R+ L G+ LA+N AG V L +RPE+++L Sbjct: 248 LPAHLLDRRGDSCTVKLGRGETVEALAVNVGAAG---TPVSLSIRPERVLL 295 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: 346 Number of extensions: 12 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: 369 Length adjustment: 30 Effective length of query: 356 Effective length of database: 339 Effective search space: 120684 Effective search space used: 120684 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