Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 253 bits (646), Expect = 6e-72 Identities = 129/253 (50%), Positives = 177/253 (69%), Gaps = 3/253 (1%) Query: 21 LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMSPKDRDIA 80 LK+I L I GEF +GPSGCGK+TL+ IAG T GA+ + DISG+ RD+ Sbjct: 34 LKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTIGGRDISGLPAHKRDVG 93 Query: 81 MVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQLSGGQ 140 MVFQSYAL+P M+VR N+AFGL+ R++P AEI+ V L+ ++HL R+P QLSGGQ Sbjct: 94 MVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVGLKHLADRRPSQLSGGQ 153 Query: 141 QQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAM 200 QQRVA+ R + PK+ L DEPLSNLDAKLRV+MR E+ + ++L TT++VTHDQ EA Sbjct: 154 QQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRKLGLTTIFVTHDQEEAN 213 Query: 201 TLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRLLALLD 260 T+ D++AVM+DGI+QQ GTP+++Y++PANLFVA F+G+ N + +++ DG A + Sbjct: 214 TICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGT--ANVLEGQVRAVDGG-TAFVM 270 Query: 261 SGQARCELPLGMQ 273 G LP G++ Sbjct: 271 GGGVPIPLPHGVE 283 Lambda K H 0.319 0.138 0.393 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: 400 Number of extensions: 18 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: 371 Length adjustment: 30 Effective length of query: 356 Effective length of database: 341 Effective search space: 121396 Effective search space used: 121396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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