GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Marinobacter guineae M3B

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_099619082.1 CLH62_RS15420 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_002744735.1:WP_099619082.1
          Length = 393

 Score =  259 bits (663), Expect = 7e-74
 Identities = 154/397 (38%), Positives = 236/397 (59%), Gaps = 9/397 (2%)

Query: 4   VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63
           V I  + RTP+G   G+L+ VR+ DL A  +KA IE +  +Q   V EV  GC   AG  
Sbjct: 6   VVIAGSARTPMGGMMGSLSSVRSPDLGAAAIKAAIERS-GLQPADVQEVIMGCVLPAGL- 63

Query: 64  NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123
            +  AR A   +G+P+S    T+N++C SGM A+  A   I +G   + IAGG+E+MS+A
Sbjct: 64  GQAPARQASRASGIPDSSGCTTINKMCGSGMQAVIMAHDQIKAGTNNIMIAGGMENMSQA 123

Query: 124 PFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDA 183
           P+++ KA +G    M++    +        ++  Y    M   A   AD Y +SR   D 
Sbjct: 124 PYLLPKARAG----MRMGHGQVMDSMFLDGLEDAYEGGLMGVFAQRTADKYDISRQAMDE 179

Query: 184 FALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPVNGP 243
           FA+ S QK+ AA   G+F +EIVPV ++ + G+T V+ DE        E +  LKP    
Sbjct: 180 FAIGSLQKSLAAIENGWFRDEIVPVTVSGRGGDTEVDTDEQ-PGNAKPEKIPHLKPAFAK 238

Query: 244 DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVR 303
           D +VTA N+S ++DGA+AL+LASA      GLTP+AR++  A+    P    + P+ A+ 
Sbjct: 239 DGSVTAANSSSISDGASALVLASAAEADARGLTPQARIVAHATHARLPSEFTLAPIGAIE 298

Query: 304 KLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGA 363
           K+ ++ G +V D D+ E+NEAFA   LA + EL +   A +VN +GGA ALGHP+G SG+
Sbjct: 299 KVLKKAGWSVDDVDLFEINEAFAVVTLAAINELKL--PAEKVNVHGGACALGHPIGSSGS 356

Query: 364 RLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           R+++T ++ L++ G ++G+A++C+G G+G A+AIE +
Sbjct: 357 RIIVTLMNALKQRGLKRGVASLCIGGGEGTAVAIELI 393


Lambda     K      H
   0.318    0.134    0.383 

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: 390
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: 400
Length of database: 393
Length adjustment: 31
Effective length of query: 369
Effective length of database: 362
Effective search space:   133578
Effective search space used:   133578
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