GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Pseudomonas fluorescens FW300-N2E2

Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate Pf6N2E2_2889 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)

Query= TCDB::O30494
         (367 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2889
          Length = 386

 Score =  305 bits (782), Expect = 1e-87
 Identities = 167/362 (46%), Positives = 237/362 (65%), Gaps = 13/362 (3%)

Query: 1   MANLKIKNLQKGFEGFSI---IKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSE 57
           MA L+++N+ K + G  +   +K I+L + D EF++ VGPSGCGKSTL+  IAGLE ++ 
Sbjct: 1   MATLELRNVNKTY-GVGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITG 59

Query: 58  GTIELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEA 117
           G I +  +D++ ++P  RD+AMVFQ+YALYP MSVR+N+ F L +  +++  ++ +V   
Sbjct: 60  GAIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQAAIDEEVTRV 119

Query: 118 ARILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELA 177
           A++L++  LL RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+ 
Sbjct: 120 AKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK 179

Query: 178 RLHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTP 237
            +H+ L+ T +YVTHDQ+EAMTL DKV V+  G I+Q G+P ++Y  PANLFVA F+G+P
Sbjct: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSP 239

Query: 238 KMGFLKGKVTRVDGQGCEVQLDAGTL---ISLPLSGASLSVGSAVTLGIRPEHLEIASP- 293
            M F+  ++ R DG+   + LD+G     + + +  A L     V LG+RPE + +A   
Sbjct: 240 PMNFIPLRLQRKDGRLLAL-LDSGQARCELPMGMQDAGLE-DREVILGMRPEQIMLAGSE 297

Query: 294 --GQTTLTVTADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHL 351
             G  T+     V E  G DT   V   N   +  R+  D+A Q GETL L  DP+   L
Sbjct: 298 PNGLPTIRAEVQVTEPTGPDTLVFV-NLNDTKVCCRLAPDVAPQPGETLTLQFDPSKVLL 356

Query: 352 FD 353
           FD
Sbjct: 357 FD 358


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: 404
Number of extensions: 17
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.

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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 (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:

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. 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