Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= TCDB::O30494 (367 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 302 bits (773), Expect = 1e-86 Identities = 170/380 (44%), Positives = 247/380 (65%), Gaps = 16/380 (4%) Query: 1 MANLKIKNLQKGFEGF--SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEG 58 MA L+++N+ K + +K I+L + + EF++ VGPSGCGKSTL+ IAGLE ++ G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 59 TIELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAA 118 I + +D++ ++P RD+AMVFQ+YALYP MSVR+N+ F L + + + ++++V A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 Query: 119 RILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178 ++L++ LL RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPK 238 +H+ L+ T +YVTHDQ+EAMTL DKV V+ G I+Q G+P E+Y+ PAN FVA F+G+P Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 Query: 239 MGFLKGKVTRVDGQGCEVQLDAGTL---ISLPLSGASLSVGSAVTLGIRPEHLEIAS-PG 294 M F+ ++ R DG+ LD+G ++L + A L V LG+RPE + +A+ G Sbjct: 241 MNFVPLRLQRKDGR-LVALLDSGQARCELALNTTEAGLE-DRDVILGLRPEQIMLAAGEG 298 Query: 295 QTTLTVTAD--VGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLF 352 + ++ A+ V E G DT V N + R+ D+A Q GETL L DP+ LF Sbjct: 299 DSASSIRAEVQVTEPTGPDTLVFV-QLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLF 357 Query: 353 DTD-----GVAVAVPLRAAA 367 D + G A ++P + A Sbjct: 358 DANTGERLGTASSLPAQGHA 377 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: 384 Number of extensions: 19 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