GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Pseudomonas fluorescens GW456-L13

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PfGW456L13_2498 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2498
          Length = 400

 Score =  462 bits (1188), Expect = e-134
 Identities = 229/400 (57%), Positives = 299/400 (74%), Gaps = 6/400 (1%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M EAVIVSTARTPIGKA+RGA N TE   L GH +  AV+RAGI+P EV+DV++GAA QQ
Sbjct: 1   MKEAVIVSTARTPIGKAFRGAFNDTEAPQLGGHVVREAVRRAGIEPGEVDDVIIGAAAQQ 60

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G    N+ R   +  GLP + AG  ++RQC+SGL +IA+AA+ ++ D ++IAV GG ESI
Sbjct: 61  GTQSYNLGRLCAIAGGLPASVAGMAVERQCSSGLMSIAMAAKGIMCDEIDIAVAGGLESI 120

Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180
           SLVQN   N +     ++  +    Y+ M++TAE V+ RYGISR+ QDEYS +SQ RTA 
Sbjct: 121 SLVQNKHKNLYRNQSGSVIELDPHAYIPMIETAEIVSARYGISRDEQDEYSYQSQLRTAQ 180

Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAV---- 236
           AQ  G+F+ E+AP++++  + DKATG  S++ +TL +DE  R +TT + L  L+ V    
Sbjct: 181 AQSAGRFDRELAPLTSRKALFDKATGETSYETVTLLRDECNRIDTTLQSLKALEPVWPGG 240

Query: 237 --RGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGP 294
               +G  ITAGNASQLSDGASA+V+MS K A  +GL+PLGI+RGM   GC  DEMGIGP
Sbjct: 241 QWSDKGGFITAGNASQLSDGASASVLMSAKMAEKRGLEPLGIYRGMAVAGCNSDEMGIGP 300

Query: 295 VFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGM 354
           ++A+P+LLKRHGL++D IGLWELNEAFA QVL+CRD LGI  E+LNVNGGAI++GHP+GM
Sbjct: 301 IYAIPKLLKRHGLTMDHIGLWELNEAFACQVLHCRDTLGIPAERLNVNGGAIAIGHPFGM 360

Query: 355 SGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           SGAR+ GHAL+EG+RR  +Y VV+MC+GGGMG+A LFE+V
Sbjct: 361 SGARMVGHALVEGQRRGLRYVVVSMCIGGGMGAAALFEVV 400


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: 511
Number of extensions: 17
Number of successful extensions: 2
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: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
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