GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlK in Pseudomonas fluorescens FW300-N1B4

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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Maltose/maltodextrin
           transport ATP-binding protein MalK (EC 3.6.3.19)
          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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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