Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate N515DRAFT_1740 N515DRAFT_1740 putative ABC transport system ATP-binding protein
Query= TCDB::O30494 (367 letters) >FitnessBrowser__Dyella79:N515DRAFT_1740 Length = 234 Score = 119 bits (297), Expect = 1e-31 Identities = 81/218 (37%), Positives = 118/218 (54%), Gaps = 11/218 (5%) Query: 11 KGFEG-FSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELDGRDITE 69 +G EG I++G+ L+V D E VG SG GK+TLL L+AGL+ S G + LDG + Sbjct: 19 RGPEGQLDILRGVSLQVRDGESFAIVGASGSGKTTLLGLLAGLDVPSGGHVGLDGHALES 78 Query: 70 VTP-AKRDL-----AMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARILEL 123 + A+ DL VFQ++ L P ++ +N+ L+L G D + EA + L Sbjct: 79 LDEEARADLRRRLVGFVFQSFHLLPALTAEENVMLPLELEGRDD--ARPRAREALEAVGL 136 Query: 124 GPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKEL 183 G P QLSGG++QRVAI RA V P++ DEP NLD + L L+++ Sbjct: 137 GARRRHYPAQLSGGEQQRVAIARAFVHGPRLLFADEPTGNLDQRTGHHVSDLLFALNRDH 196 Query: 184 QATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLEL 221 + T++ VTHD + A ++ V L+ GR+ G P EL Sbjct: 197 RTTLVLVTHDPLLA-ERCERRVELHEGRVIARG-PAEL 232 Lambda K H 0.319 0.137 0.387 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: 222 Number of extensions: 13 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: 234 Length adjustment: 26 Effective length of query: 341 Effective length of database: 208 Effective search space: 70928 Effective search space used: 70928 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: 48 (23.1 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