Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_019895416.1 A377_RS12090 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000384235.1:WP_019895416.1 Length = 363 Score = 176 bits (446), Expect = 9e-49 Identities = 103/276 (37%), Positives = 164/276 (59%), Gaps = 15/276 (5%) Query: 21 LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILVDDADISGMS----PKD 76 LK++ L+ID G+ L+GPSGCGK+TL+ IAGL+++ G++ ++ +++ P+ Sbjct: 19 LKDVNLRIDPGQIGCLLGPSGCGKTTLLRSIAGLQSVQSGSVTLEGEELTRPGFQKPPEK 78 Query: 77 RDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQL 136 R I MVFQ +AL+P +SV DN+A+GL R + + ++ V + L+ + R P QL Sbjct: 79 RHIGMVFQDFALFPHLSVADNVAYGL--RDLKGNQRNQRVQELLALVGLPDSGRRYPHQL 136 Query: 137 SGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQ 196 SGGQQQRVA+ RALA +P + L DEP S LD +LR + E++ + + T + VTH+Q Sbjct: 137 SGGQQQRVALARALAPKPAVLLLDEPFSGLDVELRESLAREVRHILKSEGMTALMVTHNQ 196 Query: 197 IEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRLL 256 EA + D+V VM++G + Q+ TP ++Y+ P + F+A FIG + + D L+ Sbjct: 197 NEAFAMADRVGVMQEGRLLQWDTPYNLYHEPHHAFIADFIGQG----VLITGSVCDCHLV 252 Query: 257 ALLDSGQARCELPLGMQDAGLEDREVILGIRPEQII 292 + G + LPLG Q V + +RP+ I+ Sbjct: 253 H-TELGLLKAHLPLGSQPG----EAVSVLVRPDDIL 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: 359 Number of extensions: 15 Number of successful extensions: 3 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: 363 Length adjustment: 30 Effective length of query: 356 Effective length of database: 333 Effective search space: 118548 Effective search space used: 118548 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 Apr 09 2024. 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