GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Phaeobacter inhibens BS107

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate GFF398 PGA1_c04090 beta-ketoadipyl-CoA thiolase PaaJ

Query= SwissProt::Q0AVM3
         (396 letters)



>FitnessBrowser__Phaeo:GFF398
          Length = 400

 Score =  330 bits (847), Expect = 3e-95
 Identities = 179/397 (45%), Positives = 255/397 (64%), Gaps = 6/397 (1%)

Query: 4   EVVLVGACRTPVGTFGGTLKDVGSAQLGAI-VMGEAIKRAGIKAEQIDEVIFGCVLQAG- 61
           +  +  A RTP+G +GG L  + +  L A+ +   A +   +    +D+VI G   QAG 
Sbjct: 2   DAFICDATRTPIGRYGGALSQLRTDDLAALPIAALAARNPDVDWSSLDDVILGDANQAGE 61

Query: 62  LGQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121
             +NVAR   + AG+P  V   TIN++C SG+ AV +A++ IKAGD D+ +AGG E+M +
Sbjct: 62  SNRNVARMAALLAGLPTTVPGTTINRLCASGMDAVGMASRGIKAGDYDMAIAGGVESMSR 121

Query: 122 APFILPNARWGYRMSMPKGDLID--EMVWGGLTDVFNGYHMGITAENINDMYGITREEQD 179
           APF++P A   +  +    D       V   + +++    M  TA+N+ + YGI+RE+QD
Sbjct: 122 APFVMPKATSAFTRANAVYDTTIGWRFVNKKMHEMYGTDSMPQTADNVAEDYGISREDQD 181

Query: 180 AFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPRKSTP-EAMAKLAPAF 237
           AF  RSQ   A A E+G F DEI PV I  +KGD +V DTDEHPR  T  E +A L    
Sbjct: 182 AFAARSQARWAAAHEAGIFNDEITPVTIPQRKGDDLVVDTDEHPRPGTSAEKLAGLKGVN 241

Query: 238 KKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPA 297
               SVTAGNASG+ND AAA+++ ++  A + G+KPMA++V   + GV+P +MG+GP+PA
Sbjct: 242 GPDKSVTAGNASGVNDGAAAILMANEAAAAKNGLKPMARIVGMTAAGVEPRIMGIGPVPA 301

Query: 298 SRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGSS 357
           +RK L + GLTID +D+IE NEAFA+Q +A  R+LG AD    VN NGGAIA+GHP+G S
Sbjct: 302 TRKVLARTGLTIDQMDVIELNEAFASQGLATLRELGVADDAPHVNPNGGAIALGHPLGMS 361

Query: 358 GARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394
           GAR+++T  Y++Q+ G +  L T+C+G G GTALI+E
Sbjct: 362 GARLVLTAAYQLQRTGGRYALCTMCVGVGQGTALILE 398


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: 497
Number of extensions: 32
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: 400
Length adjustment: 31
Effective length of query: 365
Effective length of database: 369
Effective search space:   134685
Effective search space used:   134685
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 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