GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Limnohabitans curvus MWH-C5

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_108401894.1 B9Z44_RS05530 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>NCBI__GCF_003063475.1:WP_108401894.1
          Length = 393

 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+ E+YG
Sbjct: 7   LNFQLGEDIDALRDAVRDFAQAEIAPRAAQIDHDDQFPMDLWRKMGDLGVLGITVGEEYG 66

Query: 74  GPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWI 133
           G  + Y+++ +   E+ R  +         S+L +  I   G+DAQ++KYLPKL +GE +
Sbjct: 67  GANMGYLAHMIAMEEISRASASVGLSYGAHSNLCVNQIKRNGTDAQRQKYLPKLISGEHV 126

Query: 134 GCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDE 192
           G   ++EP  GSD  SM  +A    G Y L+GSKMWITN P AD  VV+AK + E G   
Sbjct: 127 GALAMSEPGAGSDVISMKLKAEDKGGYYVLNGSKMWITNGPDADTLVVYAKTEPELGARG 186

Query: 193 IRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVK-GLRGPFTCLN 251
           +  F++EKG KG S      K+G+R S TGE+V +   VP ENIL  +  G +   + L+
Sbjct: 187 VTAFLIEKGMKGFSVAQKLDKLGMRGSHTGELVFNNVEVPAENILGGLNMGAKVLMSGLD 246

Query: 252 SARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVL 311
             R  ++ G LG  +S       Y+ DRKQFG+ +   QLIQ K+ADM T +  G     
Sbjct: 247 YERAVLSGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAY 306

Query: 312 RLGRMKD-EGTAAVEITSIMKRNSCG--------KALDIARLARDMLGGNGISDEFGVAR 362
            + +  D  GT  V       R  C         KA  +A     + GGNG  +E+ + R
Sbjct: 307 TVAKNLDLLGTDHVR----QVRKDCASVILWTAEKATWMAGEGVQIFGGNGYINEYPLGR 362

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


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: 379
Number of extensions: 17
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: 393
Length adjustment: 31
Effective length of query: 364
Effective length of database: 362
Effective search space:   131768
Effective search space used:   131768
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 24 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