Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_091519694.1 BM253_RS04260 phosphate ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_900115115.1:WP_091519694.1 Length = 248 Score = 128 bits (322), Expect = 1e-34 Identities = 86/244 (35%), Positives = 130/244 (53%), Gaps = 16/244 (6%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 L N+N ++G LKNI +S E E L+GPSGCGKSTL+ + + A + Sbjct: 5 LSAENLNISFGE--KHVLKNISVSFAEHEITALIGPSGCGKSTLLRSFNRMHDLFPDAKI 62 Query: 64 IGDQDVSGMSPKDRD---------IAMVFQSYALYPTMSVRENIEFGLKIRKMP-QADID 113 G + + DR I MVFQ +P S+ ENI +GLKI +P ++ Sbjct: 63 NGSLHLEELDLYDRHVPVTEIRKRIGMVFQKANPFPK-SIYENIAYGLKINNLPCNKEVV 121 Query: 114 AEVARVAKLL-QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRV 172 + A L ++++ L +LSGGQQQR+ + RA+A RP++ L DEP S LD + Sbjct: 122 QKALEEAYLWDEVKNDLKMPATRLSGGQQQRLCIARAVALRPEVILMDEPCSALDPVSTL 181 Query: 173 EMRTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFV 232 ++ +K H + K T V VTH+ +A + DK M G +++ GT EI+N+P N+ Sbjct: 182 KIEELIK--HLKKKYTIVIVTHNMQQAQRIADKTVFMYLGEVKEEGTTDEIFNHPKNEMT 239 Query: 233 ASFI 236 A++I Sbjct: 240 ANYI 243 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: 204 Number of extensions: 9 Number of successful extensions: 4 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: 248 Length adjustment: 27 Effective length of query: 359 Effective length of database: 221 Effective search space: 79339 Effective search space used: 79339 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: 48 (23.1 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