GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Marinobacter adhaerens HP15

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF3052 HP15_2996 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Marino:GFF3052
          Length = 398

 Score =  321 bits (823), Expect = 2e-92
 Identities = 182/401 (45%), Positives = 256/401 (63%), Gaps = 11/401 (2%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           MRDV I  A RT IG FGG L+ + AD L    +KA++E    V  DQ++EV  G    A
Sbjct: 7   MRDVVIVAARRTAIGTFGGGLSSLSADQLGTAVIKAILEET-GVAGDQINEVVLGQVLTA 65

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           G   +N AR + + AG+P S+P +T+N++C SG+ A+  A +AI  G+ E+ IAGG ESM
Sbjct: 66  G-CGQNPARQSAINAGIPASVPAMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESM 124

Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRA 179
           S+AP V+  + +G    N  + DT I     +       G+     TA+N+ + Y +SR 
Sbjct: 125 SQAPHVLPNSRNGQRMGNWSMVDTMIKDGLWDAFNDYHMGI-----TAENIVEKYGISRD 179

Query: 180 DQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALTKLK 238
           +QD FA  SQQKAAAA+ AG+F  +IVPV I  +KG+ IV +RDE  R   T E L KL+
Sbjct: 180 EQDEFAAASQQKAAAAREAGYFDGQIVPVSIPQRKGDPIVVDRDEGPRDGVTAEGLGKLR 239

Query: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298
                D TVTAGNAS +NDGAAA+++ SAE  ++ GLTP A +   A+ GV P +MG GP
Sbjct: 240 AAFKKDGTVTAGNASSLNDGAAAVMVCSAEKAEELGLTPIATIKAYANAGVDPTIMGTGP 299

Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358
           +PA ++  +  G +  D D++E NEAFA+Q ++V R++G   D  +VN NGGAIALGHP+
Sbjct: 300 IPASQRCLKLAGWSTEDLDLVEANEAFAAQAISVNRDMGW--DTGKVNVNGGAIALGHPI 357

Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399
           G SG R++++ LH++ +    KGLAT+C+G G G+ALA+ER
Sbjct: 358 GASGCRILVSLLHEMVRRDVHKGLATLCIGGGMGVALAVER 398


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: 419
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: 398
Length adjustment: 31
Effective length of query: 369
Effective length of database: 367
Effective search space:   135423
Effective search space used:   135423
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