Alignments for a candidate for treF in Cronobacter condimenti 1330

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Cronobacter condimenti 1330

Align trehalase (TreF;b3519) (EC 3.2.1.28) (characterized)
to candidate WP_032984355.1 BN137_RS11100 alpha,alpha-trehalase TreF

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



>NCBI__GCF_000319285.1:WP_032984355.1
          Length = 546

 Score =  845 bits (2183), Expect = 0.0
 Identities = 405/550 (73%), Positives = 459/550 (83%), Gaps = 5/550 (0%)

Query: 1   MLNQKIQNPNPDELMIEVDLCYELDPYELKL-DEMIEAEPEPEMIEGLPASDALTPADRY 59
           M  Q  + P  +EL  +V     +DP   +L  +  + EP+PE IEG+P+ DALTPADRY
Sbjct: 1   MFQQTTRLPFTEELAEKV----RMDPESGELIPDARDVEPQPESIEGMPSPDALTPADRY 56

Query: 60  LELFEHVQSAKIFPDSKTFPDCAPKMDPLDILIRYRKVRRHRDFDLRKFVENHFWLPEVY 119
           LELFEHVQ+++IF DSKTFPDCAPK  PL IL+ YR+ +R   FDLR+FVE HF+ P + 
Sbjct: 57  LELFEHVQASRIFADSKTFPDCAPKTSPLTILMNYRQAKRLPGFDLRRFVEEHFYFPVIN 116

Query: 120 SSEYVSDPQNSLKEHIDQLWPVLTREPQDHIPWSSLLALPQSYIVPGGRFSETYYWDSYF 179
           ++ YVSDP  +L EHID LWP+LTR+P +H+  SSLL LPQ+YIVPGGRF+ETYYWDSYF
Sbjct: 117 TNPYVSDPNRTLTEHIDNLWPILTRQPHEHLENSSLLPLPQAYIVPGGRFTETYYWDSYF 176

Query: 180 TMLGLAESGREDLLKCMADNFAWMIENYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGV 239
           TMLGLAESGR DLL+CMADNFAWMIENYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGV
Sbjct: 177 TMLGLAESGRNDLLRCMADNFAWMIENYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGV 236

Query: 240 RGARRYLDHLKMEYAFWMDGAESLIPNQAYRHVVRMPDGSLLNRYWDDRDTPRDESWLED 299
           RGARRYLDHL MEYAFWMDGAE+L P QA+RHVV+MPDG LLNRYWDDRDTPRDESW ED
Sbjct: 237 RGARRYLDHLMMEYAFWMDGAENLEPGQAWRHVVKMPDGVLLNRYWDDRDTPRDESWRED 296

Query: 300 VETAKHSGRPPNEVYRDLRAGAASGWDYSSRWLRDTGRLASIRTTQFIPIDLNAFLFKLE 359
           VETAK SGRP NEVYRDLRAGAASGWDYSSRWLRD  RLASIRTT F+P+DLNAFL+KLE
Sbjct: 297 VETAKLSGRPANEVYRDLRAGAASGWDYSSRWLRDPDRLASIRTTHFLPVDLNAFLYKLE 356

Query: 360 SAIANISALKGEKETEALFRQKASARRDAVNRYLWDDENGIYRDYDWRREQLALFSAAAI 419
           +AIANI+ LKG   T  +FR+KA  RR+A NRYLWDDE G YRDYDWRR +LA FSAA +
Sbjct: 357 TAIANIAQLKGIPATATVFRKKAIDRREACNRYLWDDEMGSYRDYDWRRGRLASFSAACV 416

Query: 420 VPLYVGMANHEQADRLANAVRSRLLTPGGILASEYETGEQWDKPNGWAPLQWMAIQGFKM 479
           VPLYVG+A++ QADR++  VR RLL+PGGIL ++ ET +QWDKPNGWAPLQWMAIQGFK 
Sbjct: 417 VPLYVGLASYAQADRISVNVRERLLSPGGILTTDVETEQQWDKPNGWAPLQWMAIQGFKN 476

Query: 480 YGDDLLGDEIARSWLKTVNQFYLEQHKLIEKYHIADGVPREGGGGEYPLQDGFGWTNGVV 539
           YGDD L D IA +WL+TV +FY E HKLIEKYHIAD  PR GGGGEYPLQDGFGWTNGV 
Sbjct: 477 YGDDPLADIIANNWLRTVKRFYNENHKLIEKYHIADYSPRPGGGGEYPLQDGFGWTNGVT 536

Query: 540 RRLIGLYGEP 549
           RRLI LYGEP
Sbjct: 537 RRLIALYGEP 546


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: 1232
Number of extensions: 54
Number of successful extensions: 1
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: 546
Length adjustment: 36
Effective length of query: 513
Effective length of database: 510
Effective search space:   261630
Effective search space used:   261630
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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 2024 update 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