GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Sphingomonas koreensis DSMZ 15582

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate Ga0059261_2888 Ga0059261_2888 acetyl-CoA acetyltransferases

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__Korea:Ga0059261_2888
          Length = 393

 Score =  317 bits (811), Expect = 5e-91
 Identities = 189/404 (46%), Positives = 250/404 (61%), Gaps = 15/404 (3%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M++ LI+  VRT IG + GAL +V A DLGA+ +   IAR   +   AV  V+ G    +
Sbjct: 1   MSDVLILSGVRTAIGDFGGALKNVPAADLGALVIGEAIAR-AGIAADAVGHVVMGNVIPS 59

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
              +  +AR+AA+ AG+PV+VP  T+NRLCGSGL A+ SAA+ +  GE G+ +AGG E+M
Sbjct: 60  TPSDAYLARVAAVRAGVPVAVPALTVNRLCGSGLQAIISAAQGIALGECGVAVAGGAENM 119

Query: 121 SRAPFVMGKSEQAFGRSA---EIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNIS 177
           S+AP  +  +   FG+     ++ D       + + +   F    M  TAENVAAQ  I 
Sbjct: 120 SQAPHYVASAR--FGQKMGDIQMLDA------LTRTLSDPFDQVHMGVTAENVAAQCGID 171

Query: 178 RADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAK 237
           RA QD  A+ S  + A AIA GR   +IV VEI  R G   + + DEH R + TLE +A+
Sbjct: 172 RAAQDEAAVESHRRGARAIAEGRFRDQIVPVEIKSRGGTV-MFDTDEHVRAEVTLEDMAR 230

Query: 238 LGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGI 297
           L   F++ G+VTAGNASG+NDGA A++L S E AQR G K  AR++G   AGVEPR+MG+
Sbjct: 231 LRPAFQRDGTVTAGNASGINDGAAAVVLGSPEEAQRLGAKPLARILGWGHAGVEPRVMGL 290

Query: 298 GPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGH 357
           GPV A    L   G+ L  +DVIE NEAFAAQ  AV  +LG   D E+ N NG  I+LGH
Sbjct: 291 GPVEAVPIALRRAGVTLDRIDVIESNEAFAAQACAVSAQLGF--DPEKTNVNGSGISLGH 348

Query: 358 PLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           P+G +GA      L+EL+   GR  L TMCIG GQGIAL+IER+
Sbjct: 349 PVGATGAINTVKLLYELQRSGGRLGLVTMCIGGGQGIALVIERL 392


Lambda     K      H
   0.319    0.134    0.384 

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: 489
Number of extensions: 22
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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