GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Paraburkholderia bryophila 376MFSha3.1

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate H281DRAFT_05493 H281DRAFT_05493 4-aminobutyrate---pyruvate transaminase

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05493 H281DRAFT_05493
           4-aminobutyrate---pyruvate transaminase
          Length = 462

 Score =  345 bits (884), Expect = 2e-99
 Identities = 178/435 (40%), Positives = 261/435 (60%), Gaps = 7/435 (1%)

Query: 21  HLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATR 80
           HL   T+      +G  ++ + +G+ ++D  G + +++M+GLWC  +G+    L  AATR
Sbjct: 19  HLHSQTNLPVHQHRGPLVMCRGDGICVYDETGKEYIESMSGLWCAALGFSDRRLAAAATR 78

Query: 81  QMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWAT 140
           Q+  LP+Y+ F       V  LA+ +A + P     +FF  SGSEANDT+ ++   Y   
Sbjct: 79  QLETLPYYHTFNHRVPDVVARLAERVAAIVPLEDPKIFFASSGSEANDTMTKIAWSYHRA 138

Query: 141 KGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYGEG-GDMS 199
            G+P+++ +I    G+HGSTV G SL G+  +H     P+ GI+H+  P++Y  G  + +
Sbjct: 139 LGKPERRKMIAHKKGFHGSTVMGASLSGLPHMHAAFGLPVEGILHVECPHFYRNGRSNET 198

Query: 200 PDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILF 259
             EF      +LE  I   G   +AAFI+EPI GAGGVIVPP  Y+P ++++L K+ IL 
Sbjct: 199 EAEFVARLVAELEALIAREGAGTIAAFISEPILGAGGVIVPPAGYFPAVQKVLRKHGILM 258

Query: 260 IADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLN----Q 315
           ++DE+ICGFGRTG+WFG+Q  G  PD+M  AK L+SGY+P+  VV+  EI   L     +
Sbjct: 259 LSDEIICGFGRTGDWFGAQGAGFVPDMMSCAKTLSSGYVPISAVVISGEIYSALQSESAR 318

Query: 316 GGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEA 375
            G F HGFTYSGHPVAAAVALE + I +E    E+ + E   YL  R   LA HPLVGE 
Sbjct: 319 SGPFGHGFTYSGHPVAAAVALEAVTIYQEMNAPERTQ-ELGAYLHDRLASLAGHPLVGEI 377

Query: 376 RGVGMVAALELVKNKKTRERF-TDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVIDPS 434
           RG G++A +ELV +K TR  F ++  VG         +GLI+R +GD + +SPP ++   
Sbjct: 378 RGRGLIAGIELVSDKDTRAPFRSEAHVGATVEARARAHGLILRNMGDVIALSPPFIVTRD 437

Query: 435 QIDELITLARKCLDQ 449
           +ID ++    + LD+
Sbjct: 438 EIDLIVQKLTRALDE 452


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: 575
Number of extensions: 29
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: 462
Length adjustment: 33
Effective length of query: 423
Effective length of database: 429
Effective search space:   181467
Effective search space used:   181467
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 paper from 2022 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