GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Xanthobacter autotrophicus Py2

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_012112924.1 XAUT_RS04530 3-oxoadipyl-CoA thiolase

Query= SwissProt::Q0AVM3
         (396 letters)



>NCBI__GCF_000017645.1:WP_012112924.1
          Length = 402

 Score =  317 bits (811), Expect = 5e-91
 Identities = 175/393 (44%), Positives = 250/393 (63%), Gaps = 13/393 (3%)

Query: 12  RTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL-GQNVARQ 69
           RTP+G + G LKDV +  L A  +    +R  G+  E +D+VI GC  QAG   ++VAR 
Sbjct: 11  RTPIGRYAGALKDVRADDLAAHPIRVLKERNPGVDWEAVDDVILGCANQAGEDNRDVARM 70

Query: 70  CMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDKAPFILPNA 129
             + AG+P      T+N++CGSGL AV + A+ I  GDAD+I+AGG E+M +APF+   A
Sbjct: 71  AALLAGLPVSAPGTTVNRLCGSGLDAVGIGARAIMTGDADLIVAGGVESMTRAPFVQGKA 130

Query: 130 RWGYRMSMPKGDLIDEMV-WGGLTDVFNGYH----MGITAENINDMYGITREEQDAFGFR 184
           +  +     + ++ D  + W  +  +    +    M  T EN+ + + ++R +QD F +R
Sbjct: 131 QEAFSR---QAEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDFQVSRADQDLFAYR 187

Query: 185 SQTLAAQAIESGRFKDEIVPVVIKGKKGDIV-FDTDEHPR-KSTPEAMAKLAPAFKK-GG 241
           SQ     A ++G F  EI P+ +KGKKG ++  + DEHPR ++T E +A L   F+K GG
Sbjct: 188 SQQRVKAAQDAGFFAREIAPIEVKGKKGAVIRVEADEHPRAETTLEQLAGLKAPFRKAGG 247

Query: 242 SVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPASRKA 301
           +VTAGNASG+ND A A+I+ S+  A + G+ P A+VVS    GV P +MG+GP PA+RK 
Sbjct: 248 TVTAGNASGVNDGAGALILASEAAAKKYGLTPRARVVSVVQAGVPPRIMGIGPAPATRKL 307

Query: 302 LEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGSSGARI 361
           LEK GL + DIDLIE NEAFAAQ++AV R LG  D  E VN NGGAIA+GHP+G SGAR+
Sbjct: 308 LEKNGLALADIDLIELNEAFAAQALAVLRQLGLPDDAEHVNPNGGAIALGHPLGMSGARL 367

Query: 362 LVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
            +T +  ++ RG  + +AT+CIG G G A ++E
Sbjct: 368 AMTAVSALEVRGGTRAVATMCIGVGQGIAALIE 400


Lambda     K      H
   0.317    0.135    0.387 

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: 475
Number of extensions: 20
Number of successful extensions: 5
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: 396
Length of database: 402
Length adjustment: 31
Effective length of query: 365
Effective length of database: 371
Effective search space:   135415
Effective search space used:   135415
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 Apr 09 2024. 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