GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Novosphingobium barchaimii LL02

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_059153518.1 V474_RS22780 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>NCBI__GCF_001046635.1:WP_059153518.1
          Length = 596

 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 93/322 (28%), Positives = 146/322 (45%), Gaps = 57/322 (17%)

Query: 114 FGSDAQKEKYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVP---GGYSLSGSKMWI 170
           + SD  K  YLPK+ +G+W G   LTEP+ G+D G + T+A  VP     Y LSGSK++I
Sbjct: 140 YASDELKAFYLPKMVSGDWSGTMCLTEPHCGTDLGMLRTKA--VPQDDDSYKLSGSKIFI 197

Query: 171 T--NSPIAD--VFVVWAKLDE--DGRDEIRGFILEK----------GCKGLSAPAIHGKV 214
           +     + +  V +V A+L +  +G   I  FI+ K             G+S  AI  K+
Sbjct: 198 SAGEHDLTENIVHLVLARLPDAPEGVKGISLFIVPKYLPKDDGTPGPSNGVSVAAIEHKM 257

Query: 215 GLRASITGEIVLDEA---FVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHI 271
           GL+AS T ++  D++    V +    PH KG+   FT +N+ R  +    LG  E+ +  
Sbjct: 258 GLKASATCQLNFDDSTGWLVGK----PH-KGMEAMFTMMNTERVSVGVQGLGVGEAAYQS 312

Query: 272 ARQYVLDRKQFGRPLAANQ---------LIQKKLADMQTEITLGLQGVLRLGRMKDEGTA 322
           A  Y  DR Q GR L+  +         ++   +  M   +    +G   LG        
Sbjct: 313 AVWYAKDRLQ-GRSLSGVKNPKGPADPIIVHPDVRRMLMTMRAYNEGCRALGGWVSRALD 371

Query: 323 AVE-----------------ITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLV 365
           A                   +T ++K        + A LA  + GG+G   E GV +++ 
Sbjct: 372 AERYSTDPEVKQRAADFIALMTPVVKALFTDLGYENANLAVQVYGGHGYIAETGVEQYVR 431

Query: 366 NLEVVNTYEGTHDIHAL-ILGR 386
           +  +   YEGT+ I AL ++GR
Sbjct: 432 DGRIAMIYEGTNGIQALDLVGR 453


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: 516
Number of extensions: 29
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 395
Length of database: 596
Length adjustment: 34
Effective length of query: 361
Effective length of database: 562
Effective search space:   202882
Effective search space used:   202882
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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