Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 207 bits (526), Expect = 5e-58 Identities = 127/308 (41%), Positives = 178/308 (57%), Gaps = 20/308 (6%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA + L + K YG L + L ++ GE L+GPSGCGK+ L+ IAG ET G Sbjct: 1 MADITLAGIGKAYGAHA--VLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAG 58 Query: 61 AILVDDADISG------MSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDE 114 I + +S + P RD+ +VFQ YA++P MSV DNI + LK+ +P AE Sbjct: 59 TISIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTR 118 Query: 115 EVARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEM 174 +V +++ + L +R P QLSGGQQQRVA+ RAL RP + L DEPL NLDA LR EM Sbjct: 119 QVLETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEM 178 Query: 175 RTEMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKD-GIIQQFGTPKDIYNNPANLFVA 233 R E+K + + L T +YVTHDQ A+ + D++A+M G I+Q GTP +I+ PA+ FV Sbjct: 179 RFEIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVF 238 Query: 234 SFIGSPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIIL 293 F+G NF+P R R +A+L +G + +P G+ D E + G RP + L Sbjct: 239 RFMG--VANFLPAR-----RRGMAMLAAGGEQ-PVPWGLPDGDAE--HWMAGFRPSDVRL 288 Query: 294 ANGEANGL 301 A + +GL Sbjct: 289 AR-QGDGL 295 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: 370 Number of extensions: 17 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: 366 Length adjustment: 30 Effective length of query: 356 Effective length of database: 336 Effective search space: 119616 Effective search space used: 119616 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