GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Psychrobacter cryohalolentis K5

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_011513566.1 PCRYO_RS06325 acyl-CoA dehydrogenase

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



>NCBI__GCF_000013905.1:WP_011513566.1
          Length = 384

 Score =  204 bits (519), Expect = 3e-57
 Identities = 128/366 (34%), Positives = 193/366 (52%), Gaps = 7/366 (1%)

Query: 26  VRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGLNYVCYGL 85
           + D+  QF  ++L P       +++    I  +M E+GL G TIPE+YGG G+       
Sbjct: 11  ITDTIRQFVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGGLGVTMEEEVT 70

Query: 86  IAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFGLTEPNHG 145
           +A E+ R    +RS++   + +    +   GTEAQKQKYLP+LASGE IG F LTEP+ G
Sbjct: 71  LAFELGRTSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIGSFCLTEPDSG 130

Query: 146 SDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD-----AGDIRGFVLEKGW 200
           SD  S+ T A K    Y + G+K +ITN+P A VF V A+ D     +G I  F++E   
Sbjct: 131 SDAASLKTTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGGISAFIVESDT 190

Query: 201 QGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGL--KGPFTCLNSARYGISWG 258
            G++   I  K+G + + T +++ DN  VP + +   V G+  K     L+  R  I+  
Sbjct: 191 PGITLGKIDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVLDKGRLHIAAA 250

Query: 259 ALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGRMKDEG 318
           + GAA      A  Y ++R+QFG+P+A  QLIQ  LAD + EI  A    L   R++DEG
Sbjct: 251 STGAATRMLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMVLDASRLRDEG 310

Query: 319 TAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDVH 378
              V  +S  K  +      +A  A  + GG G   ++G+ R   ++ +   YEGT  + 
Sbjct: 311 KDVVTESSCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLYRLYEGTTQIQ 370

Query: 379 ALILGR 384
            +I+ R
Sbjct: 371 QIIIAR 376


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: 369
Number of extensions: 14
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: 384
Length adjustment: 30
Effective length of query: 363
Effective length of database: 354
Effective search space:   128502
Effective search space used:   128502
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.

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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