GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Dinoroseobacter shibae DFL-12

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate 3609683 Dshi_3066 acetyl-CoA acetyltransferase (RefSeq)

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



>FitnessBrowser__Dino:3609683
          Length = 391

 Score =  300 bits (767), Expect = 6e-86
 Identities = 169/402 (42%), Positives = 244/402 (60%), Gaps = 15/402 (3%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M +V I  A RT +G FGG+ A   A DL +  L+AL+     ++  +V E   G     
Sbjct: 1   MTNVVIASAARTAVGSFGGSFANTPAHDLGSAVLEALVA-RAGIEKGEVSETILGQVLTG 59

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           G+  +N AR A + AGLP+      LN++C SG+ A+    + I  G+ E+  AGG E+M
Sbjct: 60  GQ-GQNPARQAHINAGLPQESAAWGLNQVCGSGLRAVALGAQHIQLGDAEIVCAGGQENM 118

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIG---WRFINPLMKSQYGVDSMPETADNVADDYQVS 177
           + +P V          +MK  D+ I    W   N           M +TA+NVA+ +Q+S
Sbjct: 119 TLSPHVANLRAGQKMGDMKFIDSMIRDGLWDAFNGY--------HMGQTAENVAEKWQIS 170

Query: 178 RADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKL 237
           R  QD FA+ SQ KA AAQ AG F +E+V   I  +KG+ +V++DE++R   T+EA+ KL
Sbjct: 171 REMQDEFAVASQNKAEAAQKAGKFDDEVVAFTIKTRKGDIVVDKDEYIRHGATMEAMQKL 230

Query: 238 KPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIG 297
           +P    D +VTA NASG+NDGAA ++L SAE  +K G+TP AR+   A+ G+ P +MG+G
Sbjct: 231 RPAFTKDGSVTAANASGLNDGAAGVLLMSAENAEKRGITPMARIASYATAGLDPSIMGVG 290

Query: 298 PVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHP 357
           P+ A RK  E+ G  V D D++E NEAFA+Q  AV +++G   D   VN NGGAIA+GHP
Sbjct: 291 PIYASRKALEKAGWKVDDLDLVEANEAFAAQACAVNKDMGW--DPAIVNVNGGAIAIGHP 348

Query: 358 LGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399
           +G SGAR++ T L ++++   +KGLAT+C+G G G+AL +ER
Sbjct: 349 IGASGARVLNTLLFEMQRRDAKKGLATLCIGGGMGVALCVER 390


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: 395
Number of extensions: 18
Number of successful extensions: 4
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: 391
Length adjustment: 31
Effective length of query: 369
Effective length of database: 360
Effective search space:   132840
Effective search space used:   132840
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