Alignments for a candidate for xad in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Pseudomonas simiae WCS417

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate GFF2156 PS417_11000 dihydroxy-acid dehydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1668
         (594 letters)



>FitnessBrowser__WCS417:GFF2156
          Length = 578

 Score =  444 bits (1142), Expect = e-129
 Identities = 258/594 (43%), Positives = 354/594 (59%), Gaps = 25/594 (4%)

Query: 6   KHRLRSEQWFNDPAHADMTALYVERYM-NYGMTREELQSGRPIIGIAQTGSDLTPCNRHH 64
           K  LRS QWF     AD        +M N G+   +   G+PIIGI  T S+LTPCN H 
Sbjct: 5   KPGLRSAQWFGT---ADKNGFMYRSWMKNQGIADHQFH-GKPIIGICNTWSELTPCNAHF 60

Query: 65  LELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVVL 124
            ++A+ VK G+ +AGG P+EFPV    E + RPTA L RNLA + + E + G P+DGVVL
Sbjct: 61  RQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVL 120

Query: 125 TTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDY 184
            TGCDKTTPA LM AA+ D+PAIV++GGPML+G HKG+ IGSGTV+W     + AG I  
Sbjct: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITL 180

Query: 185 EGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKR 244
           + F+      S S G CNTMGTA +M  +AEALG SLP  A+IPA    R  +A+ +G R
Sbjct: 181 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR 240

Query: 245 ICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIG 304
             ++VR+D++ S+I+T++AFENAI V +A+G S+N   HL AIA  +GVEL L+DW RIG
Sbjct: 241 AVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIG 300

Query: 305 EDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRL-HEDCATVSGKTIGEIVSNS- 362
             +P +V+  P+G++L E F+ AGG+P+V+  L +A  + H +  TV+GK++GE   +S 
Sbjct: 301 RGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPHPNALTVNGKSLGENTQDSP 360

Query: 363 LTSNTDVIHPFDTPLKHRAGFIVLSGNFFD-SAIMKMSVVGEAFRKTYLSEPGAENSFEA 421
           +    +VI   D P++   G  VL GN     A++K S    A  +              
Sbjct: 361 IYGQDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAASPALMQ-----------HRG 409

Query: 422 RAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDS 481
           RA+VFE  + Y ARI+DP LD+D   ILV++  G  GYPG AEV NM  PA L+ QG+  
Sbjct: 410 RAVVFENFDMYKARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTD 469

Query: 482 LPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQ 541
           +  + D R SGT+    +L+++PEAA GG LA +K  D +++D     ++L I DAE+A 
Sbjct: 470 MVRISDARMSGTAYGTVVLHVAPEAAAGGPLATVKEGDWIELDCANGRLHLDIPDAELAA 529

Query: 542 RRREWIPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGE-PRHSH 594
           R  +  P        +++LY   V Q   G           V  R  E PRHSH
Sbjct: 530 RMADLAPPQKLIVGGYRQLYIDHVLQADQG-----CDFDFLVGCRGAEVPRHSH 578


Lambda     K      H
   0.319    0.135    0.407 

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: 976
Number of extensions: 65
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: 594
Length of database: 578
Length adjustment: 37
Effective length of query: 557
Effective length of database: 541
Effective search space:   301337
Effective search space used:   301337
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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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