GapMind for catabolism of small carbon sources

 

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

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Ac3H11_2991 Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2991
          Length = 396

 Score =  211 bits (536), Expect = 4e-59
 Identities = 135/384 (35%), Positives = 204/384 (53%), Gaps = 15/384 (3%)

Query: 14  LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYG 73
           L+ QL +D   +RDA   +AQ ++APR  +  + +     ++R+MG++G+LG T+PEQYG
Sbjct: 10  LNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYG 69

Query: 74  GPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWI 133
           G  + Y+++ +   E+ R  +         S+L +  I   G++AQK KYL KL +GE +
Sbjct: 70  GAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHV 129

Query: 134 GCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDE 192
           G   ++EP  GSD  SM  +A    G Y L+GSKMWITN P AD  VV+AK + E G   
Sbjct: 130 GALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARG 189

Query: 193 IRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHV-KGLRGPFTCLN 251
           +  F++EKG KG S      K+G+R S TGE+V  +  VP EN+L  + +G +   + L+
Sbjct: 190 VTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLD 249

Query: 252 SARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVL 311
             R  +  G LG  +S       Y+ DRKQFG+ +   QLIQ K+ADM T +  G     
Sbjct: 250 YERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAY 309

Query: 312 RLGRMKDE-GTAAVEITSIMKRNSCG--------KALDIARLARDMLGGNGISDEFGVAR 362
            + +  D  GT  V       R  C         KA  +A     + GGNG  +E+ + R
Sbjct: 310 TVAKNLDMLGTDHVR----QVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGR 365

Query: 363 HLVNLEVVNTYEGTHDIHALILGR 386
              + ++     GT +I  +++GR
Sbjct: 366 LWRDAKLYEIGAGTSEIRRMLIGR 389


Lambda     K      H
   0.320    0.138    0.414 

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: 377
Number of extensions: 16
Number of successful extensions: 4
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: 395
Length of database: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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