GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Sphingomonas koreensis DSMZ 15582

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Ga0059261_4052 Ga0059261_4052 Acyl-CoA dehydrogenases

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__Korea:Ga0059261_4052
          Length = 385

 Score =  186 bits (473), Expect = 8e-52
 Identities = 121/379 (31%), Positives = 194/379 (51%), Gaps = 3/379 (0%)

Query: 14  LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDA-AIFREMGEIGLLGPTIPEQY 72
           +D  L++   M+RD    +A+ ++ P   +    +      ++  MGE+GL G T+ E++
Sbjct: 6   MDFALSETAEMIRDTTQRFAKERIEPLAAKIDAEDWFPRDELWTAMGELGLHGITVDEEF 65

Query: 73  GGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEW 132
           GG GL Y+ + +   EV R  +         S+L +  I  + S AQK KYLP+L +GE 
Sbjct: 66  GGLGLGYLEHVIACEEVSRASASIGLSYGAHSNLCVNQISRWASPAQKAKYLPRLISGEH 125

Query: 133 IGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDE 192
           +G   ++E   GSD  SM  RA      Y L+G+K WITN+  AD  VV+AK  E  R  
Sbjct: 126 VGSLAMSEAGAGSDVVSMKLRAEHKGDRYVLNGTKFWITNAAYADTLVVYAKTGEGSRG- 184

Query: 193 IRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRGP-FTCLN 251
           I  F++EK   G S      K+G+R S T E+V D+  VPEEN++  + G  G   + L+
Sbjct: 185 ITTFLIEKDMPGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENVMGPLNGGVGVLMSGLD 244

Query: 252 SARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVL 311
             R  +A   LG  ++C  +   Y+ +RKQFG+ + + QL+Q K+ADM   +      V 
Sbjct: 245 YERTVLAGIQLGIMQACLDVVLPYLRERKQFGQAIGSFQLMQAKVADMYVALNSARAYVY 304

Query: 312 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVN 371
            + +  D G       +     +   A  +A  A   LGG G + ++ V R L + ++++
Sbjct: 305 AVAQACDAGKTTRFDAAGAILLASENAFRVAGEAVQALGGAGYTKDWPVERFLRDAKLLD 364

Query: 372 TYEGTHDIHALILGRAQTG 390
              GT++I  +++GR   G
Sbjct: 365 IGAGTNEIRRMLIGRELIG 383


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: 321
Number of extensions: 13
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: 385
Length adjustment: 31
Effective length of query: 364
Effective length of database: 354
Effective search space:   128856
Effective search space used:   128856
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