GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Pseudomonas putida KT2440

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PP_2051 PP_2051 3-ketoacyl-CoA thiolase (thiolase I)

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



>lcl|FitnessBrowser__Putida:PP_2051 PP_2051 3-ketoacyl-CoA thiolase
           (thiolase I)
          Length = 394

 Score =  456 bits (1173), Expect = e-133
 Identities = 236/395 (59%), Positives = 290/395 (73%), Gaps = 2/395 (0%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M +AVIV+TARTPIGKA RGA N  +  ++   AI  AV+RAGI+P +V+D+V+G AMQ 
Sbjct: 1   MKDAVIVATARTPIGKAMRGAFNDLKTPSMTAVAIRAAVERAGIEPAQVDDLVLGTAMQS 60

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G    N  R + L AGLP + +G T+DRQCASGL AIA AA+ ++ DG+++ +G G E I
Sbjct: 61  GTAAINPGRLSALAAGLPQSVSGQTVDRQCASGLMAIATAAKQIMVDGMQVTIGAGQEQI 120

Query: 121 SLVQN-DKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179
           SLVQ         A DPA+  +    YM ML TAE VA+RYGISRE QD Y+L+SQ+RTA
Sbjct: 121 SLVQQVHNQLASEAYDPAVLRMSEHAYMPMLQTAERVARRYGISREAQDVYALQSQQRTA 180

Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239
           AAQ  G F  EI P+  +  VVDK TG VS +++ L+QDEG RP TT   L GLK V  E
Sbjct: 181 AAQAAGLFAAEIVPVIARKKVVDKLTGVVSHEEVRLTQDEGNRPATTLADLQGLKPVV-E 239

Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299
           G  +TAGNASQLSDGASA V+M    AA  G+  LG++RG+   G  P+EMGIGPV AVP
Sbjct: 240 GGCVTAGNASQLSDGASACVLMEGALAARSGIAALGLYRGIAVAGLAPEEMGIGPVLAVP 299

Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359
           +LL++ GL+VDDIGLWELNEAFA QVLYC  +L IDP KLNVNGGAI++GHPYGMSGAR+
Sbjct: 300 KLLRQQGLTVDDIGLWELNEAFACQVLYCAQQLQIDPAKLNVNGGAIAIGHPYGMSGARM 359

Query: 360 AGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
            GHAL+EG+RRK KY VVTMCVGGGMG+AGLFE++
Sbjct: 360 VGHALLEGKRRKVKYVVVTMCVGGGMGAAGLFEVL 394


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: 480
Number of extensions: 17
Number of successful extensions: 3
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.

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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