Alignments for a candidate for treF in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Pseudomonas fluorescens FW300-N2E3

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate AO353_19630 AO353_19630 glucoamylase

Query= CAZy::ABK72415.1
         (668 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19630
          Length = 608

 Score =  372 bits (954), Expect = e-107
 Identities = 234/607 (38%), Positives = 320/607 (52%), Gaps = 37/607 (6%)

Query: 45  YGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILDR-GAGHFRLGPYGVSVPAARR- 102
           +G + D  +  L++  GSV++ C P  DSPS+F ++LD   AG F+L P    +P ARR 
Sbjct: 15  HGIIGDMRSAALVNDKGSVDFFCWPEFDSPSIFCSLLDTPDAGIFQLAP---DLPDARRE 71

Query: 103 --YLPGSLILETTWQTHTGWLIVRDALVMGPWHDIDTRSRTHRRTPMDWDAEHILLRTVR 160
             YLP + +L+T W +    + + D L +G   D D             DA  +L+R VR
Sbjct: 72  QIYLPDTNVLQTRWLSEQAVVEITDLLPVG---DND-------------DALPLLIRRVR 115

Query: 161 CVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTTNLRIGIE 220
            VSG     + C    DY R   T    G       A         P LRL  N  + + 
Sbjct: 116 LVSGHATFHLHCAVRHDYARAQTTARTDG-------ADVCFEAAQQPGLRLRANQPMQVV 168

Query: 221 GREARARTRLTEGDNVFVALSWSKHPAPQTYEEAADK-MWKTSEAWRQWINVGDFPDHPW 279
              A A   L +G +    L     P  +  +E +D  + +T + WR WI   ++    W
Sbjct: 169 QDTAVATFSLKQGQSAEFLLGALDDP--RFKDENSDLCLQRTLKFWRDWIGQSNYRGR-W 225

Query: 280 RAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFALWGLYTL 339
           R  + RSAL LK LT    GA+LAA T  LPE P G RNWDYRY+WIRD++F ++    L
Sbjct: 226 REMVNRSALALKLLTSRKHGAILAAATFGLPEIPGGARNWDYRYTWIRDASFTVYAFMRL 285

Query: 340 GLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSRPVRIGN 399
           G   EA+ +  ++        G+   L V+Y + G + L E EL HLSG+ N++PVRIGN
Sbjct: 286 GFVDEANAYMRWLHGRMSDCQGKAMKLNVLYAIDGRQELPEIELAHLSGHSNAKPVRIGN 345

Query: 400 GAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGIWEVRGE 459
            AY Q Q DI+G ++D+VYL  K  E I    W      V++    W++ D GIWE+RGE
Sbjct: 346 QAYEQAQLDIFGELMDAVYLVNKYGEAISHESWQHAIKVVDQVCDSWQQEDVGIWEMRGE 405

Query: 460 PQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLAR-GVDKRGVLTQR 518
             HF  S++MCWVALDR  +LA  +   +   +W    + I AD+      D+ G   Q 
Sbjct: 406 QHHFLHSRLMCWVALDRAIRLASKRSLPAPFARWDQTRQAIYADIWNNFWSDEHGHFVQH 465

Query: 519 YGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETD-DGLAGEE 577
            G  ALD S+LL  L RF+ A DPR  +T+ AI   L  DG+V RY  +++  DGL G E
Sbjct: 466 IGGTALDGSMLLMPLVRFVSARDPRWLSTLQAIQKTLVRDGMVYRYHNDDSQIDGLPGTE 525

Query: 578 GTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGNFPQAFT 637
           G F  CSFW +  L   G + +A    E+LL +A+PL LYAEE +    RHLGN PQA T
Sbjct: 526 GAFAACSFWYIECLARAGMVEKAHLEFEQLLRYANPLGLYAEEFDSH-ARHLGNTPQALT 584

Query: 638 HLALINA 644
           HLALI+A
Sbjct: 585 HLALISA 591


Lambda     K      H
   0.319    0.135    0.426 

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: 1128
Number of extensions: 53
Number of successful extensions: 7
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: 668
Length of database: 608
Length adjustment: 38
Effective length of query: 630
Effective length of database: 570
Effective search space:   359100
Effective search space used:   359100
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources