Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 305 bits (782), Expect = 1e-87 Identities = 166/362 (45%), Positives = 241/362 (66%), Gaps = 9/362 (2%) Query: 1 MANLKIKNLQKGFEGF--SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58 MA L+++N+ K + +K I+L + + EF++ VGPSGCGKSTL+ IAGLE ++GG Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 59 TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAA 118 I + +D++ +SP RD+AMVFQ+YALYP MSVR+N+ F L + + +A+++ +V+ A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 Query: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178 ++L++ +L RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238 +H+ L+ T +YVTHDQ+EAMT+ DKV V+ G I+Q G+P ++Y+ PAN FVA F+G+P Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 Query: 239 MGFLKGKITRVDSQGCEVQLDAG-TRVSLPLGGRHLSVGSA-VTLGIRPEHLELAK-PGD 295 M F+ ++ R D + LD+G R L L + V LG+RPE + LA GD Sbjct: 241 MNFVPLRLQRKDGR-LVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGD 299 Query: 296 CALQVTAD--VSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFD 353 A + A+ V+E G DT V+ + + R+ D+A + GETL+L D LFD Sbjct: 300 SASSIRAEVQVTEPTGPDTLVFVQ-LNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 358 Query: 354 AD 355 A+ Sbjct: 359 AN 360 Lambda K H 0.320 0.137 0.389 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: 385 Number of extensions: 17 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: 367 Length of database: 386 Length adjustment: 30 Effective length of query: 337 Effective length of database: 356 Effective search space: 119972 Effective search space used: 119972 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 (21.8 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