GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Acidovorax sp. GW101-3H11

Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate Ac3H11_2934 D-2-hydroxyglutarate dehydrogenase

Query= BRENDA::O23240
         (559 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2934
          Length = 474

 Score =  303 bits (776), Expect = 1e-86
 Identities = 176/465 (37%), Positives = 269/465 (57%), Gaps = 15/465 (3%)

Query: 104 KEILGEKNVVEDKERLETANTDWMHKYKGSSKLMLLPKNTQEVSQILEYCDSRRLAVVPQ 163
           + I+G  +V+ + + L     DW  + +G +  ++ P NTQEV+ +++ C +   A+VPQ
Sbjct: 9   RAIVGPTHVITEGD-LTAWEQDWRRRVRGKALAVVRPANTQEVAAVVKACAAVGTAIVPQ 67

Query: 164 GGNTGLVGGSVPVFD--EVIVNVGLMNKILSFDEVSGVLVCEAGCILENLATFLDTKGFI 221
           GGNTGL  GS P     ++++++  MN + S D  +  +  EAGCIL+NL       G +
Sbjct: 68  GGNTGLAVGSTPDDSGTQIVLSLTRMNAVRSVDTDNLTMTVEAGCILQNLQDVAQNAGVL 127

Query: 222 MPLDLGAKGSCHIGGNVSTNAGGLRLIRYGSLHGTVLGLEAVTANGNVLDMLGTLRKDNT 281
            PL L A+GSC IGGN+ TNAGG +++RYG+     LGLE VTA G V D L  LRKDNT
Sbjct: 128 FPLSLAAEGSCTIGGNLGTNAGGTQVVRYGNARDLCLGLEVVTAQGEVWDGLKGLRKDNT 187

Query: 282 GYDLKHLFIGSEGSLGIVTKVSILTQPKLSSVNLAFIACKDYLSCQKLLVEAKRNLGEIL 341
           GYDL+ LFIGSEG+LGI+T  ++   P+ ++   A+ A         LL  A + LG  L
Sbjct: 188 GYDLRDLFIGSEGTLGIITAATMKLYPQPAANLTAWAAAPSMEHAVALLGLAHKQLGAGL 247

Query: 342 SAFEFLDNNSMDLVLNHLDGVRNPVSSSEN--FYILIETTGSD-ETNDREKLEAFLLKSL 398
           + FE +   ++ LV  H+  +R P    +N  + +L+E + S+ E + R + E+ L  + 
Sbjct: 248 TGFEVMGQFALSLVGKHMPQLRVPFLGDDNAPWCVLLENSDSESEEHARARFESLLETAF 307

Query: 399 EKGLVSDGVIAQDINQASSFWRIREGITEALQKAGAVYKYDLSLPVEEIYNIV---NDLR 455
           E G V+D V+A+++ QA   W IRE I  A  + G   K+D+S+ +  I   V   + + 
Sbjct: 308 EMGCVTDAVVAENLTQAHQLWHIRESIPLAQAEEGLNIKHDISIQISRIPAFVAHTDAVL 367

Query: 456 GRLGDLANVMGYGHLGDGNLHLNISAAEYNDKLLGL------IEPYVYEWTSKHRGSISA 509
            R      ++ +GHLGDGNLH N+ A    D    L      +   VYE  ++  GS SA
Sbjct: 368 QREIPGVRLVNFGHLGDGNLHYNVQAPAAGDPKAFLREQEARVNHLVYEAVAEFGGSFSA 427

Query: 510 EHGLGVMKANEIFYSKSPETVALMASIKKLLDPKGILNPYKVLPH 554
           EHG+G +KA+++   +SP  + +M +IK+ LDP+G++NP +VL H
Sbjct: 428 EHGIGELKADKLAKYQSPVALGMMRAIKQALDPQGVMNPGRVLGH 472


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: 591
Number of extensions: 26
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