GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Herbaspirillum seropedicae SmR1

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate HSERO_RS01265 HSERO_RS01265 acetyl-CoA acetyltransferase

Query= BRENDA::Q8VCH0
         (424 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS01265 HSERO_RS01265 acetyl-CoA
           acetyltransferase
          Length = 398

 Score =  312 bits (800), Expect = 1e-89
 Identities = 185/392 (47%), Positives = 246/392 (62%), Gaps = 10/392 (2%)

Query: 37  DVVVVHGRRTPIGRASRGCFKDTTPDELL-SAVLTAVLQDVKLKPEQLGDISVGNVLQPG 95
           D  +V   RTPIG+A RG FK+T PD+LL  A+ +AV Q   L P+ + D  VG     G
Sbjct: 7   DAYIVAATRTPIGKAPRGMFKNTRPDDLLVRAIQSAVAQVPGLDPKLIEDAIVGCSFPEG 66

Query: 96  A-GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154
           A G  MAR A  L+G+P T+   T+NR C+SG+ A+A  A  IR G  D+ +A G ESM+
Sbjct: 67  AQGLNMARNAVLLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAESMS 126

Query: 155 L-SQRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASA 213
           +    G H +I+    ++E        MG+T+E VA+++ VSR+ QD F+LAS QKA +A
Sbjct: 127 MVPMMGFHPSININAFKDENV-GMAYGMGLTAEKVAQQWKVSREAQDEFSLASHQKAIAA 185

Query: 214 QSRGCF-----HAEIVPVTTTVLNDKGDKKTITVSQDEGVRPSTTMQGLAKLKPAFKDGG 268
           Q  G F       EIV     +   + D KT TVS DEG R  + +  LAKLKP F   G
Sbjct: 186 QEAGEFADEMTSFEIVERFPNLATGEIDVKTRTVSLDEGPRADSNLAALAKLKPVFAAKG 245

Query: 269 STTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAA 328
           S TAGNSSQ SDGA A+++      ++  L  L    S+AV GVPP++MGIGP  AIPAA
Sbjct: 246 SVTAGNSSQTSDGAGALIIVSEKILKQFNLTPLARFVSFAVRGVPPEIMGIGPKEAIPAA 305

Query: 329 LQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVV 388
           L+  GLT + ID  E+NEAFA+QA+  +  LG+   KVNP+GGAIALGHPLG TGA +  
Sbjct: 306 LKAGGLTQDQIDWIELNEAFAAQALAVIGDLGLDPSKVNPMGGAIALGHPLGATGAIRAA 365

Query: 389 TLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420
           T ++ L+R+  + YG+V+MC+GTGMGAA +FE
Sbjct: 366 TTIHALRRKNLK-YGMVTMCVGTGMGAAGIFE 396


Lambda     K      H
   0.317    0.133    0.377 

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: 411
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 424
Length of database: 398
Length adjustment: 31
Effective length of query: 393
Effective length of database: 367
Effective search space:   144231
Effective search space used:   144231
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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