GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Pseudomonas fluorescens FW300-N2E3

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate AO353_00505 AO353_00505 3-ketoacyl-CoA thiolase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_00505 AO353_00505
           3-ketoacyl-CoA thiolase
          Length = 391

 Score =  244 bits (624), Expect = 2e-69
 Identities = 158/401 (39%), Positives = 221/401 (55%), Gaps = 25/401 (6%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQG 61
           + VIV   RTP+G++  G    T    +  H I   ++R   +DP EVEDV+ G   Q  
Sbjct: 7   DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTL 66

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
             G NIAR A L   +P T AG T+ R C S + A+  AA++++    ++ V GG E + 
Sbjct: 67  EQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMG 126

Query: 122 LVQNDKMNTFHAVDP----ALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRR 177
            V     +  H VDP    +L A K    M +  TAE + K +GI+RE+QD + + S + 
Sbjct: 127 HV-----SMMHGVDPNPHMSLYAAKASGMMGL--TAEMLGKMHGITREQQDAFGVRSHQL 179

Query: 178 TAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AV 236
              A   GKF DEI P+           G +   D     DE  RPETT E LA LK A 
Sbjct: 180 AHKATVEGKFKDEIIPMQGY-----DENGFLKLFDY----DETIRPETTLESLAALKPAF 230

Query: 237 RGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVF 296
             +G T+TAG +SQ++DGAS  ++MS + A   G++P+ + R M   G +P  MG GPV 
Sbjct: 231 NPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVP 290

Query: 297 AVPRLLKRHGLSVDDIGLWELNEAFAVQVL-YCRDKLGIDP--EKLNVNGGAISVGHPYG 353
           A  + LKR GL + DI  +ELNEAFA Q L   +D   +D   EK+N++GGAI++GHP+G
Sbjct: 291 ATQKALKRAGLGIADIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFG 350

Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
            SGAR++G  L   ++    + V TMC+G G G A +FE V
Sbjct: 351 CSGARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFERV 391


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: 393
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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