GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Burkholderia phytofirmans PsJN

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate BPHYT_RS21555 BPHYT_RS21555 beta alanine--pyruvate aminotransferase

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS21555 BPHYT_RS21555 beta
           alanine--pyruvate aminotransferase
          Length = 442

 Score =  265 bits (678), Expect = 2e-75
 Identities = 154/423 (36%), Positives = 228/423 (53%), Gaps = 21/423 (4%)

Query: 24  PFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMR 83
           PFT  +Q  +   R++  A+G+Y   ++G ++LD  AGLWCVN G+GREE+V A T Q+ 
Sbjct: 16  PFTANRQF-KAAPRLLESAKGMYYRSTDGREVLDGCAGLWCVNAGHGREEIVAAITEQLS 74

Query: 84  ELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQ 143
            L F   F Q  HP   E A  +A++ PEG++ +FFT SGSE+ DT L++   Y  ++G+
Sbjct: 75  TLDFAPTF-QMGHPLAFEAATKVAELMPEGLDRIFFTNSGSESVDTALKIALAYHRSRGE 133

Query: 144 PQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQ-GDFPIPGIVHIAQPYWYGEGG-DMSPD 201
            Q+  +IGR  GYHG    G+S+GG+    +      +P + H+   +            
Sbjct: 134 GQRTRLIGRERGYHGVGFGGISVGGIAPNRKTFSGALLPAVDHLPHTHNLEHNAFTKGQP 193

Query: 202 EFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIA 261
            +G   AE+LE+ +       +AA I EP+ G+ GV++PP  Y  K+REI  K+ IL I 
Sbjct: 194 AWGAHLAEELERIVTLHDASTIAAVIVEPVAGSTGVLIPPQGYLQKLREICTKHGILLIF 253

Query: 262 DEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQGG---- 317
           DEVI  FGR G+   S+Y+G  PDL+ +AK + +  IPMG V     I + +  GG    
Sbjct: 254 DEVITAFGRVGKATASEYFGVTPDLITMAKAINNAAIPMGAVAASRTIHDSIVNGGAQGA 313

Query: 318 -EFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEAR 376
            E +HG+TYS HPVA A A+  + + + E + E+  A  AP  +     L     V + R
Sbjct: 314 IELFHGYTYSAHPVATAAAVATLDLYKREGLFERA-ATLAPTFEAAAHSLRGAKHVKDVR 372

Query: 377 GVGMVAALELVKNKKTRERFTDKGVGMLCRE---HCFRNGLIMRAVGDTMIISPPLVIDP 433
            +GM+A +EL           D   G    E    CF  G+++R  GD +  SPPL+I+ 
Sbjct: 373 NLGMIAGVELESR--------DGAPGARAYEAFVKCFEAGVLVRFTGDILAFSPPLIINE 424

Query: 434 SQI 436
            QI
Sbjct: 425 EQI 427


Lambda     K      H
   0.320    0.138    0.425 

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: 562
Number of extensions: 35
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: 456
Length of database: 442
Length adjustment: 33
Effective length of query: 423
Effective length of database: 409
Effective search space:   173007
Effective search space used:   173007
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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