Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate BPHYT_RS29175 BPHYT_RS29175 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS29175 Length = 390 Score = 315 bits (806), Expect = 2e-90 Identities = 169/365 (46%), Positives = 235/365 (64%), Gaps = 10/365 (2%) Query: 2 ATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGA 61 A + +RN+ GA ++N++L ++ GEF++L+GPSGCGKSTL++ IAGL +T G+ Sbjct: 35 ANVAVRNLTIQLGANT--VIENLDLDVQAGEFVVLLGPSGCGKSTLLHSIAGLIDVTDGS 92 Query: 62 IMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAK 121 I I +D++ PKDR IA+VFQSYALYPTMSV N+ F L+I P+A+I VAR ++ Sbjct: 93 IEIAGEDMTWADPKDRRIALVFQSYALYPTMSVERNLSFALRINGTPKAEIARRVARASE 152 Query: 122 LLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181 +LQ+ LL RKP QLSGGQ+QRVA+GRA+ R ++LFDEPLSNLDAKLR E+R E+K + Sbjct: 153 MLQLGPLLKRKPAQLSGGQRQRVAIGRAIVREADVFLFDEPLSNLDAKLRTELRRELKQL 212 Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPM 241 HQRL T +YVTHDQ+EAMTL ++AVM+ G+IQQFGTP E+Y P N FVA+F+G+P M Sbjct: 213 HQRLGATMIYVTHDQVEAMTLATRMAVMRGGVIQQFGTPAEVYARPDNLFVATFLGTPAM 272 Query: 242 NFVPLRLQRKDGRLVALLDSGQAR-CELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 N + RL+ +DG L + + TT A +LG+R E + LA G Sbjct: 273 NLIKGRLETRDGALHFCTEHWRLDVSRYPFRTTPA--NGLPCVLGVRAEDVRLAEG---- 326 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDAN 360 +S A+V + EP G ++++ + +V +G+ FD + V LFD Sbjct: 327 -ASEHAKVSLVEPMGNHRVIWLDYHGVQVASIDQTKTPLAIGDAAAFSFDSTHVSLFDEA 385 Query: 361 TGERL 365 G RL Sbjct: 386 GGARL 390 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: 402 Number of extensions: 12 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: 386 Length of database: 390 Length adjustment: 30 Effective length of query: 356 Effective length of database: 360 Effective search space: 128160 Effective search space used: 128160 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