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_2157 3-ketoacyl-CoA thiolase (EC 2.3.1.16)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2157
          Length = 394

 Score =  387 bits (994), Expect = e-112
 Identities = 202/394 (51%), Positives = 261/394 (66%), Gaps = 1/394 (0%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M E VIV + RT + K++RG  N T    +  H ++  + R GIDP  VED ++GA   +
Sbjct: 1   MREVVIVDSVRTGLAKSFRGKFNMTRPDDMAAHCVDALLARTGIDPASVEDCIVGAGSNE 60

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           GA G NI R   + + L + TAG T++R C+SGLQAIA+AA  +     +I V GG ESI
Sbjct: 61  GAQGFNIGRNVAVLSRLGIGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESI 120

Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180
           SL     +NT + ++P L+     +Y  M  TAE VA+RY +SR+ QD Y+L+SQ+RTA 
Sbjct: 121 SLTMKS-VNTDNLINPLLKEQVPGIYFPMGQTAEIVARRYNVSRQEQDLYALQSQQRTAE 179

Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEG 240
           AQ  G F DEI P+S K  V DKATG     D  + +D+  RP+TT E L GLK V  E 
Sbjct: 180 AQAAGLFTDEIVPMSVKYRVEDKATGQAQILDGIVDRDDCNRPDTTLESLTGLKPVFAED 239

Query: 241 FTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPR 300
            ++TAGN+SQLSDGAS T++MS + A   GLKP   FRG    GC PDEMGIGPVF+VP+
Sbjct: 240 GSVTAGNSSQLSDGASMTLVMSLEKALELGLKPKAFFRGFTVAGCAPDEMGIGPVFSVPK 299

Query: 301 LLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLA 360
           LLK  GL + DI LWELNEAFA Q LY R++L ID  + NVNGG+IS+GHP+GM+G+R  
Sbjct: 300 LLKAKGLRIADIDLWELNEAFASQCLYSRNRLEIDNARYNVNGGSISIGHPFGMTGSRQV 359

Query: 361 GHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           GH + E +RR  +Y +VTMCVGGGMG+ GLFE V
Sbjct: 360 GHLVRELQRRNLRYGIVTMCVGGGMGATGLFEAV 393


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: 437
Number of extensions: 13
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: 394
Length adjustment: 31
Effective length of query: 364
Effective length of database: 363
Effective search space:   132132
Effective search space used:   132132
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.

Links

Downloads

Related tools

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