GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Dinoroseobacter shibae DFL-12

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 3607889 Dshi_1297 acyl-CoA dehydrogenase domain protein (RefSeq)

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>FitnessBrowser__Dino:3607889
          Length = 387

 Score =  206 bits (523), Expect = 1e-57
 Identities = 124/371 (33%), Positives = 194/371 (52%), Gaps = 5/371 (1%)

Query: 19  LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78
           L EE   +R+  +++AQ+++ P   E  R      A++ EMGE+GLLG T+ E YGG+G+
Sbjct: 10  LGEEVEALREMVHRWAQERVKPLAAETDRSNAFPNALWPEMGELGLLGITVDEAYGGAGM 69

Query: 79  NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138
            Y+ + +   E+ R  +         S+L +  I   GT+AQK+KYLPKL SG  +G   
Sbjct: 70  GYLAHTVAVEEISRASASIGLSYGAHSNLCVNQIKLNGTDAQKEKYLPKLVSGAHVGALA 129

Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD--AGD--IRGF 194
           ++E   GSD   M  RA K +  YRL G+K WITN P AD  VV+AK D  AG   I  F
Sbjct: 130 MSEAGAGSDVVGMKLRAEKRNDHYRLNGTKYWITNGPDADTLVVYAKTDPEAGSKGITAF 189

Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF-PDVRGLKGPFTCLNSARY 253
           ++EK   G S      K+G+R S T E++ ++V VP EN+   + RG+    + L+  R 
Sbjct: 190 LIEKEMAGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVAVLMSGLDYERV 249

Query: 254 GISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGR 313
            +S   +G    C      Y  +R+QFG P+   QL+Q K+ADM T +  A      + +
Sbjct: 250 VLSGVNIGIMAGCLDEVMPYMTERRQFGEPIGNFQLMQGKIADMYTAMNSARAYAYEVAK 309

Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373
             D G    +  +     +  + + +A  A   +GG G  ++  VAR   + +++    G
Sbjct: 310 ACDRGEVTRQDAAACVLYASEEGMKVAHQAVQAMGGAGFLNDSPVARMFRDAKLMEIGAG 369

Query: 374 THDVHALILGR 384
           T ++  +++GR
Sbjct: 370 TSEIRRMLVGR 380


Lambda     K      H
   0.320    0.137    0.413 

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: 331
Number of extensions: 13
Number of successful extensions: 3
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: 393
Length of database: 387
Length adjustment: 31
Effective length of query: 362
Effective length of database: 356
Effective search space:   128872
Effective search space used:   128872
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.

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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