Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate GFF3990 Psest_4063 sulfate ABC transporter, ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__psRCH2:GFF3990 Length = 334 Score = 217 bits (553), Expect = 3e-61 Identities = 130/311 (41%), Positives = 186/311 (59%), Gaps = 17/311 (5%) Query: 3 TLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAI 62 ++E+ ++NK +G L I L I+ GE + L+GPSGCGK++L+ IAGLET G+I Sbjct: 2 SIEISHINKRFGQF--QALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSI 59 Query: 63 MIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVAR---- 118 + +DVS +DR++ VFQ YAL+ M+V EN+ FGL+++ Q +A +A Sbjct: 60 VFHGEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHE 119 Query: 119 VAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178 + L+Q++ L +R P QLSGGQ+QR+A+ RALA PK+ L DEP LDAK+R E+R + Sbjct: 120 LLGLVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWL 179 Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGS 238 +H+ + T+V+VTHDQ EAM + D++ VM G+I+Q GTP E+Y NPA++FV F+G Sbjct: 180 ARLHEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLGD 239 Query: 239 PPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDV-ILGLRPEQIMLAAGE 297 RLQ D R V A A+ AG E RD+ LG + AG+ Sbjct: 240 AN------RLQLDDQRSVLFRPHEVALSREAVAEHLAG-EVRDIRPLGALTRVTLKVAGQ 292 Query: 298 GDSASSIRAEV 308 A I AEV Sbjct: 293 ---AEPIEAEV 300 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: 330 Number of extensions: 15 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: 334 Length adjustment: 29 Effective length of query: 357 Effective length of database: 305 Effective search space: 108885 Effective search space used: 108885 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: 49 (23.5 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