Aligments for a candidate for dopDH in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for dopDH in Pseudomonas simiae WCS417

Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate GFF2806 PS417_14315 2,5-dioxovalerate dehydrogenase

Query= metacyc::G1G01-1343-MONOMER
         (525 letters)



>FitnessBrowser__WCS417:GFF2806
          Length = 523

 Score =  813 bits (2100), Expect = 0.0
 Identities = 411/524 (78%), Positives = 453/524 (86%), Gaps = 2/524 (0%)

Query: 1   MPLTGNLLIGQRPVTGSRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRE 60
           M LTG +LIGQ   TG+R+AIRA++P T   +EPAY GG  EHVAQACALAWAAFD YRE
Sbjct: 1   MTLTGKMLIGQHATTGNREAIRAVNPATDTPMEPAYPGGDREHVAQACALAWAAFDGYRE 60

Query: 61  TSLEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAG 120
           TSLE RA FLEAIA  IEALGD LI+RAV ETGLP+ARIQGERGRTC QLRTFARTVRAG
Sbjct: 61  TSLEARAAFLEAIAAHIEALGDELIERAVAETGLPRARIQGERGRTCGQLRTFARTVRAG 120

Query: 121 EWLDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180
           EWLDVR+D A P+RQPLPR DLRQR +ALGPVAVFGASNFPLAFSVAGGDTASALAAGCP
Sbjct: 121 EWLDVRVDPAQPQRQPLPRPDLRQRHIALGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180

Query: 181 VVVKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFT 240
           VVVKAH AHPGTSELVG+AVAQA++ CGLPEGVFSLLYGSGREVGIALV+DPRIKAVGFT
Sbjct: 181 VVVKAHGAHPGTSELVGRAVAQAIQACGLPEGVFSLLYGSGREVGIALVTDPRIKAVGFT 240

Query: 241 GSRSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQ 300
           GSRSGG+AL QAAQARPEPIPVYAEMSSINPV+LF AAL AR E LA+GFV SLTQGAGQ
Sbjct: 241 GSRSGGVALTQAAQARPEPIPVYAEMSSINPVYLFPAALAARGEGLAKGFVGSLTQGAGQ 300

Query: 301 FCTNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAI 360
           FCTNPGLVI  QGPAL RFI+ A+  +   AAQTMLTPGIF A+ +G+ AL +  HA+  
Sbjct: 301 FCTNPGLVIGVQGPALDRFISTASELLPTCAAQTMLTPGIFKAFDSGVTALTE--HARVS 358

Query: 361 TSGQAGQGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQ 420
             G A +GPNQ QA LFVT A+ FLA+  LQAEVFGAASL+V C  +E++ QV+EHLEGQ
Sbjct: 359 AKGLAAEGPNQGQAHLFVTPAKDFLANEQLQAEVFGAASLIVVCASNEEMHQVSEHLEGQ 418

Query: 421 LTATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480
           LTATL LD+ D+ SA+ALLP LERKAGR+LVNGWPTGVEVCDAMVHGGPFPATSD+R+TS
Sbjct: 419 LTATLHLDDDDLPSAKALLPVLERKAGRLLVNGWPTGVEVCDAMVHGGPFPATSDSRSTS 478

Query: 481 VGTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRRLLDGKRE 524
           VGTAAI RFLRPVCYQD PDALLP AL+HGNPL LRRLLDG+RE
Sbjct: 479 VGTAAIQRFLRPVCYQDFPDALLPDALQHGNPLLLRRLLDGQRE 522


Lambda     K      H
   0.319    0.134    0.391 

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: 977
Number of extensions: 27
Number of successful extensions: 2
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: 525
Length of database: 523
Length adjustment: 35
Effective length of query: 490
Effective length of database: 488
Effective search space:   239120
Effective search space used:   239120
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 17 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, or view the source code.

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