GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Erythrobacter marinus HWDM-33

Align 2-oxoisovalerate dehydrogenase subunit alpha 2, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_047092924.1 AAV99_RS06245 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

Query= SwissProt::Q84JL2
         (472 letters)



>NCBI__GCF_001013305.1:WP_047092924.1
          Length = 330

 Score =  147 bits (370), Expect = 7e-40
 Identities = 94/296 (31%), Positives = 147/296 (49%), Gaps = 7/296 (2%)

Query: 146 IFYEAQRQGRLSFYATAIGEEAINIASAAALTPQDVIFPQYREPGVLLWRGFTLQEFANQ 205
           ++ + + +G L  Y   IGEEA+ +    AL PQD +   YRE G  L RG +      +
Sbjct: 35  LYTQEKIRGFLHLY---IGEEAVAVGVMEALAPQDAVVATYREHGHALVRGVSAGAIMAE 91

Query: 206 CFGNKSDYGKGRQMPVHYGSNKLNYFTVSATIATQLPNAVGAAYSLKMDKKDACAVTYFG 265
            +G +     GR   +H       ++  +A +   LP A G A + K+  +   +V +FG
Sbjct: 92  MYGKQEGCSGGRGGSMHLFDAATRFYGGNAIVGGGLPLAAGLALADKLAGRSNVSVCFFG 151

Query: 266 DGGTSEGDFHAALNIAAVMEAPVLFICRNNGWAISTPTSDQFRSDGVVVKGRAYGIRSIR 325
           +G  +EG+FH  LN+AA+ + PVLF+C NN +A+ T          +  K   Y ++S  
Sbjct: 152 EGAVAEGEFHETLNLAALWQLPVLFVCENNLYAMGTALDISESETDISAKAACYRMQSDA 211

Query: 326 VDGNDALAMYSAVHTAREMAIREQ-RPILIEALTYRVGHHSTSDDSTRYRSAGEIEWWNK 384
           VDG + + + +A   A   AIRE  RP  +E  TYR   HS  D    YR+  E+E W K
Sbjct: 212 VDGMNVVNVEAAARRA-VAAIRETGRPYFLECRTYRFRAHSMFDPQL-YRAKAEVEEW-K 268

Query: 385 ARNPLSRFRTWIESNGWWSDKTESDLRSRIKKEMLEALRVAEKTEKPNLQNMFSDV 440
            R P++RF+TW    G  +D     +   +  E+ EA+  AE      + ++F +V
Sbjct: 269 GRGPITRFKTWALEAGELNDPDIEAIEQEVAHEIAEAVAFAEAGTWEPVGHLFHNV 324


Lambda     K      H
   0.318    0.132    0.394 

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: 335
Number of extensions: 10
Number of successful extensions: 2
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: 472
Length of database: 330
Length adjustment: 31
Effective length of query: 441
Effective length of database: 299
Effective search space:   131859
Effective search space used:   131859
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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