GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_954
          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:

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:

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:

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:

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