Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 199 bits (506), Expect = 1e-55 Identities = 142/388 (36%), Positives = 204/388 (52%), Gaps = 29/388 (7%) Query: 3 TLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAI 62 +L +R + + YGA L + L I EGEF+ L+GPSG GKS+L+ +AGL+ G + Sbjct: 2 SLSIRQLTRRYGAFA--ALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDV 59 Query: 63 MIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIR----KMPQADIDAEVAR 118 + D+ + + RDI +VFQ YAL+P M+V +NI FGL++R + + DI A V Sbjct: 60 LRDGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVED 119 Query: 119 VAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178 + + +Q+E L R P QLSGGQ+QRVA+ RALA P + L DEP LDA++R +R + Sbjct: 120 LLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWL 179 Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGS 238 + + + L TTV VTHDQ EA+ L D+V VM G I+Q G P EIY PA FV F+G Sbjct: 180 RDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGR 239 Query: 239 PPMNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEG 298 N + ++R L G+ +LA R++ LRPE + LA+ Sbjct: 240 --ANRIRGHVERDRLHLGGHSFQGELPGDLA---------GREIEAWLRPEHLALAS--- 285 Query: 299 DSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRL---APDVAPQ---VGETLTLQFDPS 352 +Q + GP + ++ + A +VA +GE +TLQ P Sbjct: 286 RGLGGWTGRLQHLDLAGPVARARLAMHGDGLVLDAEWNAAEVAAHGLAIGEVVTLQ--PR 343 Query: 353 KVLLF-DANTGERLGTASSLPAQGHADN 379 + LF D G R PA HAD+ Sbjct: 344 EFTLFADVPGGVRRLRFVPAPAGPHADS 371 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: 347 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: 384 Length adjustment: 30 Effective length of query: 356 Effective length of database: 354 Effective search space: 126024 Effective search space used: 126024 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: 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