GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Acidovorax sp. GW101-3H11

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ac3H11_2303 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2303
          Length = 392

 Score =  271 bits (692), Expect = 3e-77
 Identities = 169/396 (42%), Positives = 229/396 (57%), Gaps = 21/396 (5%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M + VIVS ART +GK + GAL  T  + L    I  A+ RAG+   ++ +V+MG  +  
Sbjct: 1   MEDIVIVSAARTAVGK-FGGALAKTPASELGAIVIREAIARAGLSSDQIGEVIMGQVLAA 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G  G N AR+A ++AG+   T   TI+  C SGL+A+ LAA++V +   +I V GG E++
Sbjct: 60  GV-GQNPARQASMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSDIVVAGGQENM 118

Query: 121 SLVQN--------DKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEY 170
           SL  +         +M  +  VD  +     DVY    M  TAE VAK YGI+R+ QD  
Sbjct: 119 SLAPHVLNGSRDGQRMGDWKMVDSMIVDGLWDVYNQYHMGITAENVAKAYGITRDMQDAL 178

Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230
           +L SQ++ AAAQ  GKF DEI  +S      D          I  + DE    +T AE L
Sbjct: 179 ALGSQQKAAAAQDAGKFADEIVGVSLAQKKGDP---------ILFNADEYLNRKTNAEAL 229

Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290
           AGL+    +  ++TAGNAS L+DGA+A V+MS K AAA GLKPL       + G +P  M
Sbjct: 230 AGLRPAFDKAGSVTAGNASGLNDGAAAVVVMSAKKAAALGLKPLARIAAFGTSGLDPATM 289

Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350
           G+GPV A  + L+R G +  D+ L+ELNEAFA Q      +L IDP K+NVNGGAI++GH
Sbjct: 290 GMGPVPASRKALQRAGWNAADVDLFELNEAFAAQACAVNKELAIDPAKVNVNGGAIAIGH 349

Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMG 386
           P G SG R+    L E +RR AK  +  +C+GGGMG
Sbjct: 350 PIGASGCRILVTLLHEMQRRDAKKGLAALCIGGGMG 385


Lambda     K      H
   0.316    0.134    0.378 

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: 439
Number of extensions: 21
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: 395
Length of database: 392
Length adjustment: 31
Effective length of query: 364
Effective length of database: 361
Effective search space:   131404
Effective search space used:   131404
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 (21.6 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