Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= TCDB::O30494 (367 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 372 bits (954), Expect = e-107 Identities = 202/376 (53%), Positives = 261/376 (69%), Gaps = 16/376 (4%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELD 63 LK+ N+ K G I++ + LE+ EFVVFVGPSGCGKSTLLRLIAGL+ + G + +D Sbjct: 4 LKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLID 63 Query: 64 GRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARILEL 123 GR + ++ P +R + MVFQ+YALYPHMSV N+SF L LA DK + +V + A+IL+L Sbjct: 64 GRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQL 123 Query: 124 GPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKEL 183 LL+RKPK+LSGGQRQRVA+GRA+ R P I LFDEPLSNLDA+LRVQMR E+ARLH L Sbjct: 124 DKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRL 183 Query: 184 QATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLK 243 +TMIYVTHDQVEAMTLADK+VVLN GR+EQVGSP ELY +PA+ FVAGFLG+P+M FL Sbjct: 184 GSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFLS 243 Query: 244 GKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEI-ASPGQTTLTVTA 302 ++ + G+ V + SLP ++L+ G+ ++LGIRPEH+ + A+ G + VTA Sbjct: 244 ARL-QTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVVVTA 302 Query: 303 DVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDGVAVA-- 360 E LGS+T+ H+ T EPL R Q G+ + L LD + HLFD DGVA++ Sbjct: 303 --VEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVALSRH 360 Query: 361 ----------VPLRAA 366 VPLR+A Sbjct: 361 PHAIETLPAGVPLRSA 376 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: 437 Number of extensions: 21 Number of successful extensions: 3 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: 381 Length adjustment: 30 Effective length of query: 337 Effective length of database: 351 Effective search space: 118287 Effective search space used: 118287 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 Apr 09 2024. 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