GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Pseudomonas fluorescens FW300-N2C3

Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate AO356_24000 AO356_24000 hydroxyacid dehydrogenase

Query= BRENDA::O23240
         (559 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24000
          Length = 474

 Score =  281 bits (718), Expect = 5e-80
 Identities = 172/459 (37%), Positives = 259/459 (56%), Gaps = 13/459 (2%)

Query: 106 ILGEKNVVEDKERLETANTDWMHKYKGSSKLMLLPKNTQEVSQILEYCDSRRLAVVPQGG 165
           ++G K+V +  E      TD   +Y G     + P +T+EV+ ++  C +    VV QGG
Sbjct: 12  LVGAKHV-QGSEDAAPYLTDKQGRYVGQVIAAVHPASTEEVAAVVRACAATDTPVVVQGG 70

Query: 166 NTGLVGGSVPVFD--EVIVNVGLMNKILSFDEVSGVLVCEAGCILENLATFLDTKGFIMP 223
           NTGL+GG+ P      +++ +  MN++ + D  +  L  EAGCIL+ +       G + P
Sbjct: 71  NTGLIGGATPDSSGRAMLLLLDRMNRVRAVDTDNDTLTVEAGCILQTVQDVAREAGRLFP 130

Query: 224 LDLGAKGSCHIGGNVSTNAGGLRLIRYGSLHGTVLGLEAVTANGNVLDMLGTLRKDNTGY 283
           L LGA+GSC +GGN+ TNAGG  ++RYG+     LGLE VTA G V D L  LRKDNTGY
Sbjct: 131 LSLGAEGSCTLGGNLGTNAGGTAVLRYGNTRELTLGLEVVTARGEVWDGLRGLRKDNTGY 190

Query: 284 DLKHLFIGSEGSLGIVTKVSILTQPKLSSVNLAFIACKDYLSCQKLLVEAKRNLGEILSA 343
           DL+ LFIGSEG+LGI+T  ++   P   +   A +A         LL  A+   G  L+A
Sbjct: 191 DLRDLFIGSEGTLGIITAATLKLFPLPKAQATALLAFDSLEQAVALLSHARAGFGASLTA 250

Query: 344 FEFLDNNSMDLVLNHL-DGVRNPVSSSENFYILIETTGS-DETNDREKLEAFLLKSLEKG 401
           FE L    + L+     DG R   S+ + ++ L+E + +  E++ RE  E  L ++ E+ 
Sbjct: 251 FELLSAECLALLREQFPDGPRPFASARQPWFALLELSDNHSESHAREVFEQVLGEAFEQH 310

Query: 402 LVSDGVIAQDINQASSFWRIREGITEALQKAGAVYKYDLSLPVEEIYNIVNDLRGRLGD- 460
           L++D +IA+ + Q+ +FW++RE +++A ++AG   K+D+S+P+ ++   V      L + 
Sbjct: 311 LLADALIAESLVQSQAFWQLRENMSDAQKRAGRNMKHDISVPISQVVAFVAHTDALLQEQ 370

Query: 461 LANVMGY--GHLGDGNLHLNI-----SAAEYNDKLLGLIEPYVYEWTSKHRGSISAEHGL 513
              V  Y  GHLGDGNLH N+     S  + +      +   V++    H GSISAEHG+
Sbjct: 371 FPGVRHYTFGHLGDGNLHYNVAHPLDSTVDAHMGHYAALSRLVHDSAHAHGGSISAEHGI 430

Query: 514 GVMKANEIFYSKSPETVALMASIKKLLDPKGILNPYKVL 552
           G  K NE+   KS   + LM  IK+ LDP+ +LNP KVL
Sbjct: 431 GQRKVNELGRYKSTVELDLMHRIKQALDPRNLLNPGKVL 469


Lambda     K      H
   0.317    0.136    0.390 

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: 588
Number of extensions: 30
Number of successful extensions: 5
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: 559
Length of database: 474
Length adjustment: 35
Effective length of query: 524
Effective length of database: 439
Effective search space:   230036
Effective search space used:   230036
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 (21.6 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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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