GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_05493
          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:

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