Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4847 Length = 367 Score = 306 bits (783), Expect = 8e-88 Identities = 163/361 (45%), Positives = 239/361 (66%), Gaps = 7/361 (1%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA L+++N+ K + +K I+L + + EF++ VGPSGCGKSTL+ IAGLE ++GG Sbjct: 1 MANLKIKNLQKGFEGF--SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I + +D++ +SP RD+AMVFQ+YALYP MSVR+N+ F L + + +A+++ +V A Sbjct: 59 TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVGEAA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++L++ +L RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+ Sbjct: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H+ L+ T +YVTHDQ+EAMT+ DKV V+ G I+Q G+P ++Y+ PAN FVA F+G+P Sbjct: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 M F+ ++ R +G+ +L R L L+ + V LG+RPE + LA GD Sbjct: 239 MGFLKGKVTRVNGQSCEVLLDAGTRITLPLSGANLSVGGA-VTLGIRPEHLELAQ-PGDC 296 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTK-VCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359 + A+ V+E G DT V + + + R+ D+A + GETL+L D LFDA Sbjct: 297 TLQVTAD--VSERLGSDTFCHVLTSSGEALTMRVRGDLASRYGETLSLHLDAEHCHLFDA 354 Query: 360 N 360 + Sbjct: 355 D 355 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: 389 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: 367 Length adjustment: 30 Effective length of query: 356 Effective length of database: 337 Effective search space: 119972 Effective search space used: 119972 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