GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Sphingomonas koreensis DSMZ 15582

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases

Query= BRENDA::Q96329
         (436 letters)



>FitnessBrowser__Korea:Ga0059261_2164
          Length = 394

 Score =  233 bits (595), Expect = 6e-66
 Identities = 136/385 (35%), Positives = 209/385 (54%), Gaps = 2/385 (0%)

Query: 46  SDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI 105
           +D +  +  LT EE+ +R   R   ++ + P +T  +    F   I  ++G +G+ G +I
Sbjct: 10  ADPFALDAQLTDEERMVRDAARAYAQERLLPRVTRAFLDENFDREIMSEMGQLGLLGPTI 69

Query: 106 -KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLA 164
            + YG  GL   A  +   E+  VD+   + + V SSL M  I   G+E QK KYLP L 
Sbjct: 70  PETYGGAGLGYVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLL 129

Query: 165 QLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT 224
               V C+ LTEPD GSD   + T A K++GG++I G K WI NS  AD+ +++A++   
Sbjct: 130 SGEWVGCFGLTEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAH 189

Query: 225 NQ-INGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKV 283
              I GF+++K   GL A KI  K+ LR    G+I++  V V ++  LP V   +     
Sbjct: 190 GGGIKGFVLEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVSEDALLPEVQGLKGPFGC 249

Query: 284 LAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLM 343
           L  +R  +AW  +G +   +    +Y  +R+QFG PLAA QL Q KL  M   +      
Sbjct: 250 LNRARYGIAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGLQA 309

Query: 344 GWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEP 403
             R  ++++ G++ P   S+ K     KA E A + R++ GGNGI A+F V +   +LE 
Sbjct: 310 ALRAGRMFDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINLET 369

Query: 404 IYTYEGTYDINTLVTGREVTGIASF 428
           + TYEGT+D++ L+ GR +TGIA+F
Sbjct: 370 VNTYEGTHDVHGLILGRAITGIAAF 394


Lambda     K      H
   0.319    0.133    0.399 

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: 338
Number of extensions: 14
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: 436
Length of database: 394
Length adjustment: 31
Effective length of query: 405
Effective length of database: 363
Effective search space:   147015
Effective search space used:   147015
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 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