GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Sphingobium czechense LL01

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_066607952.1 V473_RS17395 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>NCBI__GCF_001046645.1:WP_066607952.1
          Length = 381

 Score =  234 bits (598), Expect = 2e-66
 Identities = 150/371 (40%), Positives = 206/371 (55%), Gaps = 9/371 (2%)

Query: 13  DMVRDVATR----EIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVLTL 68
           DM+RD A R     IAP A E+D K  FP        +LGL    +    GG  +G L  
Sbjct: 13  DMIRDSAARFSADRIAPLAAEIDAKDWFPRELWPAMGELGLHGITVSEEDGGLGLGYLEH 72

Query: 69  ALILEELGRVCASTALLLIAQTDGML-PIIHGGSPELKERYLRRFAGESTLLTALAATEP 127
            +  EE+ R  AS  L   A ++  +  I   G+ E K +YL +      +  +LA +E 
Sbjct: 73  VVAQEEVARASASIGLSYGAHSNLCVNQIRRWGNAEQKAKYLPKLISGDHV-GSLAMSEA 131

Query: 128 AAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFVVEK 187
            AGSD+++MK +A ++GD+Y++NG K +ITN   AD +VVYA T   +GSKGI+ F++EK
Sbjct: 132 GAGSDVVSMKLKAEKKGDRYILNGTKFWITNAPYADTLVVYAKTG--EGSKGITTFLIEK 189

Query: 188 GTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVFCAA 247
              G   G+   KMGMRGS  +EL F++ EVP ENI+G    G   LM  L   R   A 
Sbjct: 190 DMKGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENIMGPLNGGVGILMSGLDYERTVLAG 249

Query: 248 QAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAELLDD 307
             +GI Q  LD  + + ++R QFG+PI     +Q  VADM  A+ ++R      A   D 
Sbjct: 250 IQLGIMQACLDTVLPYVRERQQFGRPIGAFQLMQAKVADMYVALNSARAYVYAVARACDS 309

Query: 308 GDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYTGTNQ 367
           G K      + A  +AS+ AM+V  +AVQ LGG+GY K+  VER MRDAKL  I  GTN+
Sbjct: 310 G-KTTRFDAAGAILLASENAMKVALEAVQALGGAGYTKDWPVERYMRDAKLLDIGAGTNE 368

Query: 368 ITRMVTGRALL 378
           I RM+ GR L+
Sbjct: 369 IRRMLIGRELI 379


Lambda     K      H
   0.319    0.134    0.371 

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: 323
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 380
Length of database: 381
Length adjustment: 30
Effective length of query: 350
Effective length of database: 351
Effective search space:   122850
Effective search space used:   122850
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 (21.7 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