Alignments for a candidate for treF in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Pseudomonas stutzeri RCH2

Align trehalase (TreF;b3519) (EC 3.2.1.28) (characterized)
to candidate GFF357 Psest_0358 Neutral trehalase

Query= CAZy::AAC76544.1
         (549 letters)



>FitnessBrowser__psRCH2:GFF357
          Length = 534

 Score =  591 bits (1524), Expect = e-173
 Identities = 293/515 (56%), Positives = 363/515 (70%), Gaps = 3/515 (0%)

Query: 31  LDEMIEAEPEPEMIEGLPASDALTPADRYLELFEHVQSAKIFPDSKTFPDCAPKMDPLDI 90
           + ++   +P    +  +  +D LTPA+RY ELF  VQ   IFPDSKTF DCAP   P  I
Sbjct: 1   MTDIAPCQPFTYDVSAISLADTLTPAERYQELFVAVQMQCIFPDSKTFVDCAPLQHPEAI 60

Query: 91  LIRYRKVRRHRDFDLRKFVENHFWLPEVYSSEYVSDPQNSLKEHIDQLWPVLTREPQDHI 150
           L  YR       FDL  FV  HF L E+   E+V++P +SL EHID+LWP+LTR PQDH 
Sbjct: 61  LADYRGRCDEPGFDLAAFVREHFSLYEMPVKEFVANPDDSLAEHIDRLWPILTRHPQDHP 120

Query: 151 PWSSLLALPQSYIVPGGRFSETYYWDSYFTMLGLAESGREDLLKCMADNFAWMIENYGHI 210
             SSLL LP  Y+VPGGRF+E YYWDSYFTMLGL ESG  DLL+ MADNFA++I+ YGH+
Sbjct: 121 EHSSLLPLPHDYVVPGGRFTELYYWDSYFTMLGLDESGHCDLLRAMADNFAYLIDTYGHV 180

Query: 211 PNGNRTYYLSRSQPPVFALMVELFEEDGVRGARRYLDHLKMEYAFWMDGAESLIPNQAYR 270
           PNGNRTYYL RSQPPVFALM ELFEE GV  A  YL  L  EYAFWMDGA++L P +A+R
Sbjct: 181 PNGNRTYYLGRSQPPVFALMTELFEETGVYRASDYLPQLHKEYAFWMDGADALRPGEAHR 240

Query: 271 HVVRMPDGSLLNRYWDDRDTPRDESWLEDVETAKHSGRPPNEVYRDLRAGAASGWDYSSR 330
             V + DG +LNRYWD+RDTPR+ES+ EDVETA+ S RP +EVYRDLRAGA SGWD+SSR
Sbjct: 241 RCVCLADGVVLNRYWDERDTPREESYREDVETARSSCRPRHEVYRDLRAGAESGWDFSSR 300

Query: 331 WLRDTGRLASIRTTQFIPIDLNAFLFKLESAIANISALKGEKETEALFRQKASARRDAVN 390
           WL D  RLA+IRTT  +P+DLNA L+KLE  IA +SA+K +      F ++A+AR  A++
Sbjct: 301 WLDDAHRLATIRTTSILPVDLNALLYKLERQIAELSAVKNQHACAEDFARRAAARLSAID 360

Query: 391 RYLWDDENGIYRDYDWRR-EQLALFSAAAIVPLYVGMANHEQADRLANAVRSRLLTPGGI 449
            YLW+     Y DYDW+R  Q    +AA + PL+VGMA+ EQA  +A  V++RLL PGG+
Sbjct: 361 NYLWNPNAAAYFDYDWQRGRQRDNLTAATLAPLFVGMASAEQAAAVALTVQARLLVPGGL 420

Query: 450 LASEY-ETGEQWDKPNGWAPLQWMAIQGFKMYGDDLLGDEIARSWLKTVNQFYLEQHKLI 508
             +E   +GEQWD+PNGWAPLQW+ I+G + YG D L  EI   WL  V+  +  ++KL+
Sbjct: 421 ATTEIGGSGEQWDRPNGWAPLQWIGIRGLQRYGHDALALEIEERWLTIVSHLFERENKLV 480

Query: 509 EKYHIADGVPREGGGGEYPLQDGFGWTNGVVRRLI 543
           EKY +        GGGEYPLQDGFGWTNGV R+L+
Sbjct: 481 EKY-VLRPCTEHAGGGEYPLQDGFGWTNGVTRKLM 514


Lambda     K      H
   0.319    0.138    0.434 

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: 1020
Number of extensions: 45
Number of successful extensions: 4
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: 549
Length of database: 534
Length adjustment: 35
Effective length of query: 514
Effective length of database: 499
Effective search space:   256486
Effective search space used:   256486
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: 52 (24.6 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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