GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Acidovorax sp. GW101-3H11

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate Ac3H11_4342 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)

Query= reanno::WCS417:GFF5299
         (454 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4342
          Length = 454

 Score =  272 bits (695), Expect = 2e-77
 Identities = 161/454 (35%), Positives = 243/454 (53%), Gaps = 24/454 (5%)

Query: 6   PQTREWQALSSDHHLAPFSDFKQLKEKGPRIITKAHGVYLWDSEGNKILDGMAGLWCVAI 65
           P +    A   D H  PF+  +  K K PR+I    G Y  D++G KI DG++GLWC  +
Sbjct: 13  PDSPRMDAEWLDAHWMPFTGNRNFKAK-PRMIVSGQGAYYTDADGRKIFDGLSGLWCSGL 71

Query: 66  GYGRDELADAAAKQMKELPYYNLFFQTAHPPVLELAKAISDIAPAGMNHVFFTGSGSEGN 125
           G+GR ++A+A  K    L Y +  FQ  HP    LA  + ++ PAG+++VFFTGSGSE  
Sbjct: 72  GHGRKDVAEAIGKAAATLDY-SPAFQFGHPASFALANKLKELTPAGLDYVFFTGSGSESA 130

Query: 126 DTMLRMVRHYWAIKGQPNKKTIISRKNGYHGSTVAGASLGGMTYMHE---QGDLPIPGIT 182
           DT L+M R YW  KGQ +K  +I R+ GYHG    G S+GG+    +   QG +    + 
Sbjct: 131 DTSLKMARAYWRAKGQASKTRLIGREKGYHGVNYGGISVGGIVGNRKTFGQG-IEADHLP 189

Query: 183 HIAQPYWFGEGGDMSPEEFGVWAANQLEEKILELGVDNVGAFIAEPIQGAGGVIVPPATY 242
           H   P    + G    E+ G   A++L + I      N+ A I EP  G+ GV++PP  Y
Sbjct: 190 HTQPPAGTFQKG--MAEDGGRALADKLLDVIALHDASNIAAVIVEPFSGSAGVVIPPKGY 247

Query: 243 WPRIKEILAKYDILFIADEVICGFGRTGEWFGSDFYDLKPHMMTIAKGLTSGYIPMGGLI 302
             RI+EI  + +IL I DEVI GFGR G W G++ + + P ++  AK +T+G  P+GG+I
Sbjct: 248 LERIREICTQNNILLIFDEVITGFGRCGAWTGAEAFGVTPDILNFAKQVTNGAQPLGGVI 307

Query: 303 VRDEVVEV-LNEGG-----DFNHGFTYSGHPVAAAVALENIRIMRDEKIVNRVHDETAPY 356
              E+ +  +++GG     +F HG+TYS HPVA A     + I++ E +  RV    AP+
Sbjct: 308 ATKEIYDTFISQGGPEYMLEFPHGYTYSAHPVACAAGNAVLDILQKEDMPGRV-KALAPH 366

Query: 357 LQKRLRELADHPLVGEVRGVGMLGAIEL--VQDKATRKRYEGKGVGMICRTFCFENGLIM 414
            +  +  L     V ++R  G+   I +  +  +  ++ YE           C+E G  +
Sbjct: 367 FENAVHGLKGAKHVADIRNYGLAAGITISALPSEPAKRPYE-------IAMKCWEKGFYV 419

Query: 415 RAVGDTMIISPPLVISKAEIDELVTKARQCLDLT 448
           R  GDT+ ++PP + + AEID +V+     L  T
Sbjct: 420 RYGGDTIQLAPPFISTSAEIDRMVSALGDALHET 453


Lambda     K      H
   0.320    0.139    0.426 

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: 626
Number of extensions: 32
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: 454
Length of database: 454
Length adjustment: 33
Effective length of query: 421
Effective length of database: 421
Effective search space:   177241
Effective search space used:   177241
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