GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS01265
          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 (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