GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS21555
          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:

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