GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Magnetospirillum magneticum AMB-1

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_011385596.1 AMB_RS16315 acyl-CoA dehydrogenase

Query= BRENDA::Q96329
         (436 letters)



>NCBI__GCF_000009985.1:WP_011385596.1
          Length = 392

 Score =  233 bits (594), Expect = 8e-66
 Identities = 136/384 (35%), Positives = 209/384 (54%), Gaps = 2/384 (0%)

Query: 47  DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105
           D +   D L+ +E+ IR       ++++ P + + +    F   I  ++G MG+ G +I 
Sbjct: 8   DPFLLEDQLSEDEKLIRDSAHAYCQEKLQPRVMKAFRDETFDREIMNEMGEMGLLGPTIP 67

Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165
           + YG PG++  A  + + E+ RVD+   + + V SSL M  I   G+E QK+KYLP LA 
Sbjct: 68  EEYGGPGVNHVAYGLISREVERVDSGYRSAMSVQSSLVMHPIFSYGTEEQKKKYLPRLAT 127

Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTT-T 224
              + C+ LTEPD GSD  G+ T A KV+GG+ + G K WI NS  +D+ I++A++    
Sbjct: 128 GEIIGCFGLTEPDAGSDPGGMRTRAKKVDGGYLLTGSKMWITNSPISDIAIVWAKSDAHE 187

Query: 225 NQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVL 284
            +I GFIV+K   G    KI  K+ LR    G+I+L   FVPDE  +P  +        L
Sbjct: 188 GKIKGFIVEKGIKGFTTPKIEGKLSLRASITGEIVLDEAFVPDEALMPNASGLGGPFGCL 247

Query: 285 AVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMG 344
             +R  +AW  IG +   +    +Y+ +RKQFG PLAA Q+ Q KL  M+  +       
Sbjct: 248 NKARYGIAWGVIGAAEFCWHAARQYMLDRKQFGRPLAANQIPQLKLANMMTEITLGLQAC 307

Query: 345 WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPI 404
            R+ ++ +     P   SL K     KA + A + R++ GGNGI  +F V +   +LE +
Sbjct: 308 VRVGRMMDDHTWAPEAVSLIKRNNCGKALDIARMARDMHGGNGISEEFHVIRHMVNLETV 367

Query: 405 YTYEGTYDINTLVTGREVTGIASF 428
            TYEG +D++ L+ GR +TGI +F
Sbjct: 368 NTYEGAHDVHALILGRAMTGIQAF 391


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: 368
Number of extensions: 17
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: 392
Length adjustment: 31
Effective length of query: 405
Effective length of database: 361
Effective search space:   146205
Effective search space used:   146205
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