Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 207 bits (528), Expect = 3e-58 Identities = 119/301 (39%), Positives = 177/301 (58%), Gaps = 21/301 (6%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 L L + K +G + ++L I G F L+G SGCGK+T + I+GLE + G I Sbjct: 19 LRLTGLTKKFGSFT--AVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIH 76 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 + D D++ P R + VFQ+YAL+P + + +N+AFGL+ R + + + + V + L+ Sbjct: 77 LGDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRS--VKKPVEDMLDLV 134 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 ++ HL RKP QLSGGQQQR+A+ RAL +P++ L DEPL LD KLR +M+ E+K + Sbjct: 135 ELGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQL 194 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 + T V+VTHDQ EAMT+ D +AVM G I+Q G+P ++Y NP FVA+F+G N Sbjct: 195 EVGLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQ--SNL 252 Query: 244 IPLRLQRKDGRLLALLDSGQ------ARCELPLGMQDAGLEDREVILGIRPEQIILANGE 297 I ++ G ++ + G+ ARC G VILG+RPE++ +A E Sbjct: 253 IAGTVESVSGDVVQVAAHGRSLALPAARCRTTSG---------PVILGVRPEKVRIAKTE 303 Query: 298 A 298 A Sbjct: 304 A 304 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: 356 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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