Aligments for a candidate for edd in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for edd in Acidovorax sp. GW101-3H11

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= BRENDA::Q1PAG1
         (608 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_954 Dihydroxy-acid
           dehydratase (EC 4.2.1.9)
          Length = 567

 Score =  226 bits (576), Expect = 2e-63
 Identities = 159/510 (31%), Positives = 255/510 (50%), Gaps = 29/510 (5%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127
           V + + ++ +   +   +   +     + E G   Q  G TP + DG+  G  GM+ SL 
Sbjct: 46  VGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFG-TPTISDGMAMGTEGMKYSLV 104

Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISN 187
           SREVI+      +     D  L++G CDK +PG +MG LR  ++P I+V GG +  G   
Sbjct: 105 SREVISDCIETCVGGQWMDGVLVVGGCDKNMPGGLMGMLR-ANVPAIYVYGGTILPGHYQ 163

Query: 188 KEKADVRQRY------AEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241
            +  ++   +      A GK +  +L E E ++    G+C    TANT     E +G+ L
Sbjct: 164 GKDLNIVSVFEAVGENAAGKLSDFDLKEIEKRAIPGTGSCGGMYTANTMSSAFEALGISL 223

Query: 242 PGAS-FVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           P +S   NP+    ++    A   +  + K   +  P  +IV ++S+ N++  + ATGGS
Sbjct: 224 PYSSTMANPHDEKMNSAKESAKVLIEAIKK---DIKP-RDIVTKKSIENAVAVIMATGGS 279

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN  LH  AIA AAG++ +  D   +    P L  + P+GK        AGG+  +++ L
Sbjct: 280 TNAVLHFLAIAHAAGVEWSIDDFERVRVKTPVLCDLKPSGKYLAVDLHRAGGIPQVMKVL 339

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIE-SLDENILRPVARAFSPEGG 419
           L AGLLH D  T+ G+ ++             V +D P +   D++++RP+      +G 
Sbjct: 340 LNAGLLHGDCLTIEGKTVAE------------VLKDVPDQPRADQDVIRPINNPMYAQGH 387

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           L +++GNL           L++ ++  PA VF+D+Q   +A  AG+++   V V+R+ GP
Sbjct: 388 LAILKGNLSPEGAVAKITGLKNPVITGPARVFEDEQSALEAILAGKIKAGDVMVLRYLGP 447

Query: 480 RSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARV 538
           +   GMPE+   T  L +    G  V L+TDGR SG +  +    HV+PEA  GG +A V
Sbjct: 448 KGGPGMPEMLAPTGAL-IGAGLGESVGLITDGRFSGGTWGMVVG-HVAPEAAAGGTIAFV 505

Query: 539 RDGDIIRVDGVKGTLELKVDADEFAAREPA 568
            +GD I +D  +  LEL V  +E A R  A
Sbjct: 506 HEGDSITIDARQLLLELNVSEEEIARRRAA 535


Lambda     K      H
   0.318    0.134    0.386 

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: 900
Number of extensions: 57
Number of successful extensions: 6
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: 608
Length of database: 567
Length adjustment: 37
Effective length of query: 571
Effective length of database: 530
Effective search space:   302630
Effective search space used:   302630
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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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