Alignments for a candidate for dgoD in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for dgoD in Pseudomonas fluorescens FW300-N2E3

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate AO353_03420 AO353_03420 phosphogluconate dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03420
          Length = 608

 Score =  197 bits (500), Expect = 1e-54
 Identities = 156/516 (30%), Positives = 250/516 (48%), Gaps = 49/516 (9%)

Query: 47  IGILNTWSDMTPCNGHLRELAEKVKAGVWEAGG---FPLEVPVFSASENTFRP---TAMM 100
           + I+++++DM   +       E++K  + E G    F   VP          P     + 
Sbjct: 68  VAIVSSYNDMLSAHQPYEHYPEQIKHALREIGSVGQFAGGVPAMCDGVTQGEPGMELGIA 127

Query: 101 YRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYFR 159
            R + A++   A+     D  ++L  CDK  P L+MGA     LP+I V GGPM++G   
Sbjct: 128 SREVIAMSTAVALSHNMFDAAMMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISN 187

Query: 160 GERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMA 219
            E+           +    G+ ++ E LE+E     S GTC   GTA+T   + E +G+ 
Sbjct: 188 KEKAD-------VRQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 220 LSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD---LKPSEIMTKQAFENAIRTNAAIGGS 276
           L G + +      R  + +    +I ++ K     +   EI+ +++  N+I    A GGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQITRLTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300

Query: 277 TNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRL 336
           TN  +H+ AIA   GI L+  D       VPT+ ++ P+GK  +  F  AGG+  +++ L
Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360

Query: 337 GEAGLLHKDALTV---------------SGETVWDEVKDVVNWNEDVILPAEKALTSSGG 381
            EAGLLH+D  TV               +GE VW E   + + +E+++ P  +A +  GG
Sbjct: 361 LEAGLLHEDVNTVAGHGLSRYTQEPFLENGELVWRE-GPIESLDENILRPVARAFSPEGG 419

Query: 382 IVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFED----IDDYKAKINDDNLDIDENCI 437
           + V+ GNL     V+K SA +P   V +  A+VF+D     D +KA +      ++++ +
Sbjct: 420 LRVMEGNLG--RGVMKVSAVAPEHQVVEAPAMVFQDQQDLADAFKAGL------LEKDFV 471

Query: 438 MVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSPEA 495
            VM+  GP+   GM E+  M     VL+     +  ++D RMSG A G +   +H SPEA
Sbjct: 472 AVMRFQGPRS-NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVSPEA 529

Query: 496 AVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARR 531
            VGG LA V+ GD+I +D     L L +  +E A R
Sbjct: 530 FVGGALARVQEGDIIRVDGVKGTLQLLVDADEFAAR 565


Lambda     K      H
   0.318    0.135    0.408 

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: 773
Number of extensions: 40
Number of successful extensions: 8
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: 579
Length of database: 608
Length adjustment: 37
Effective length of query: 542
Effective length of database: 571
Effective search space:   309482
Effective search space used:   309482
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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)
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