Alignments for a candidate for treF in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Trichormus variabilis ATCC 29413

Align trehalase (TreH) (EC 3.2.1.28) (characterized)
to candidate WP_011318250.1 AVA_RS07210 alpha,alpha-trehalase

Query= CAZy::BAG85338.1
         (505 letters)



>NCBI__GCF_000204075.1:WP_011318250.1
          Length = 495

 Score =  827 bits (2137), Expect = 0.0
 Identities = 385/487 (79%), Positives = 439/487 (90%)

Query: 13  DSVRAHIKKTWKTLTRSHEHLLQSAKDTKLDHKPGTPWIVYISPLEDCPNIQTVLERSLS 72
           ++VR +IK+TWKTLTRSH+HLL+SA+DTKL+H+P TPWI+YISP EDC  +++VLERSLS
Sbjct: 4   NTVRTYIKQTWKTLTRSHQHLLESAQDTKLEHQPNTPWIIYISPQEDCNTVKSVLERSLS 63

Query: 73  SKDMQQLEIRTLPAEVEAIKQHGLLYLPGPYVVPGGRFNEMYGWDSYFILLGLLHDEEWE 132
           +K+MQQ+EIRTLP+EVEAI++HGLLYLPGPYVVPGGRFNEMYGWDSYFILLGLL DEEWE
Sbjct: 64  TKEMQQIEIRTLPSEVEAIQEHGLLYLPGPYVVPGGRFNEMYGWDSYFILLGLLQDEEWE 123

Query: 133 LAQSQVDQLLYQVQHYGTILNANRTYMLSRSQPPVLSMMVLALFQHTQDEEWLRSTVPLL 192
           LAQSQVDQLLYQVQHYGTILNANRTYML+RSQPPVLSMMVLALFQHTQD+ WL+ST+PLL
Sbjct: 124 LAQSQVDQLLYQVQHYGTILNANRTYMLTRSQPPVLSMMVLALFQHTQDQAWLKSTLPLL 183

Query: 193 EQFYYYWVVPPHLNPGTGLSRFYAFGEGPAPEVVFSERDDEGKSHYDRVKEYYQTFEIDD 252
           EQFYYYWVVPPHLN  TGLSR+YA GEG APEV+FSE D+ G+SHY+RVKEYY+TFEIDD
Sbjct: 184 EQFYYYWVVPPHLNSATGLSRYYALGEGAAPEVLFSELDEAGRSHYERVKEYYKTFEIDD 243

Query: 253 YDVNLYYDREDDKLTHLFYKADRTMRESGFDITNRFGPFSADILHYAPVCLNSLLYQVEQ 312
           YDV+L+YD E D+LT LFYK DR+MRESGFDITNRFGPFS DI+HYAPVCLNSLLYQ+EQ
Sbjct: 244 YDVSLFYDSEKDELTDLFYKGDRSMRESGFDITNRFGPFSVDIVHYAPVCLNSLLYQMEQ 303

Query: 313 DLAQINAILGNEQLEKQWRDRGAYRRDRIDQFLWNEERGLYCDYHFQSGKRRCYEFATTF 372
           DL QI+ IL N +L +QW DR   RR+RI+Q+LW+EE+G+Y DYHF SGKRR YEFATTF
Sbjct: 304 DLTQIHKILDNPELAEQWSDRANIRRERINQYLWDEEKGIYLDYHFYSGKRRHYEFATTF 363

Query: 373 YPLWLGISSQAQAQRVVENLSLFEAPGGILTSTHITGNQWDAPFGWAPLTFIAVQGLHRY 432
           YPLW G+SS  QAQR+VENLSLF APGGI TST +TGNQWDAPFGWAPLT IAVQGL+RY
Sbjct: 364 YPLWTGLSSPEQAQRIVENLSLFTAPGGIFTSTRVTGNQWDAPFGWAPLTLIAVQGLYRY 423

Query: 433 GFHTEGDRIANKFLAMVIKEFERHNTLVEKYDVERCSANVSDEISFGYSSNEVGFGWTNG 492
           G+  EGD IA+KFL M I+EF ++   VEKYDVERCSA VSDEI FGYSSNE+GFGWTNG
Sbjct: 424 GYRKEGDDIAHKFLTMAIQEFTKYGFFVEKYDVERCSAQVSDEICFGYSSNEIGFGWTNG 483

Query: 493 VILELLA 499
           VILELLA
Sbjct: 484 VILELLA 490


Lambda     K      H
   0.320    0.138    0.430 

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: 1032
Number of extensions: 34
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: 505
Length of database: 495
Length adjustment: 34
Effective length of query: 471
Effective length of database: 461
Effective search space:   217131
Effective search space used:   217131
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: 52 (24.6 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 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