Align glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized)
to candidate BWI76_RS19555 BWI76_RS19555 PTS beta-glucoside transporter subunit EIIBCA
Query= CharProtDB::CH_088352 (169 letters) >FitnessBrowser__Koxy:BWI76_RS19555 Length = 619 Score = 126 bits (317), Expect = 6e-34 Identities = 56/148 (37%), Positives = 92/148 (62%) Query: 22 EIIAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIE 81 +I+AP++G ++ ++ VPD FA ++G G+AI P+ K++AP G + IF+T HA + Sbjct: 472 DILAPMTGSVLALDQVPDSTFASGLLGQGVAIIPSVGKVIAPFSGEVASIFQTKHAIGLL 531 Query: 82 SDSGVELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDTVIEFDLPLLEEKAKSTLTPVVI 141 SDSG+EL +H GIDTV+L G F +EG ++K GD ++EFD + + TP++I Sbjct: 532 SDSGIELLIHVGIDTVKLDGAPFTAHVKEGDKIKAGDLLLEFDRQAILDAGYDLATPIII 591 Query: 142 SNMDEIKELIKLSGSVTVGETPVIRIKK 169 SN D+ + L +S S P++ + + Sbjct: 592 SNSDDFRTLDMVSASAVDAGQPLLSVSR 619 Lambda K H 0.315 0.138 0.374 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: 212 Number of extensions: 9 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: 169 Length of database: 619 Length adjustment: 27 Effective length of query: 142 Effective length of database: 592 Effective search space: 84064 Effective search space used: 84064 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: 42 (21.9 bits) S2: 48 (23.1 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