GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Sinorhizobium meliloti 1021

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate SMc02228 SMc02228 acetyl-CoA acetyltransferase

Query= BRENDA::Q0KAI3
         (392 letters)



>lcl|FitnessBrowser__Smeli:SMc02228 SMc02228 acetyl-CoA
           acetyltransferase
          Length = 402

 Score =  270 bits (690), Expect = 5e-77
 Identities = 162/407 (39%), Positives = 232/407 (57%), Gaps = 20/407 (4%)

Query: 1   MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60
           M +  + D +R+P GR K   A  E+ +  L A+V++ + +RN LD   VDDVI GCV  
Sbjct: 1   MTKVFVYDHVRTPRGRGKKDGALHEVPSVRLAAKVLEAVRDRNGLDTSTVDDVIMGCVDP 60

Query: 61  AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120
             +  A   + A   AG+    P   I R C S   AV+F A  I  GA DIVIA G+ES
Sbjct: 61  VMDAGAVIPKAAAFEAGYSTRAPGMQISRFCASGLDAVNFGAAKIAQGADDIVIAGGVES 120

Query: 121 MSRVPMGSARIGQNPYGPSME--ARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHE 178
           MSRV +G +  G     PS+   A + P    QGV+A+L+A KY  SR D+D+Y+  S +
Sbjct: 121 MSRVGLGMSG-GAWFMDPSVNLPAYFMP----QGVSADLIATKYGFSRDDVDAYAVESQK 175

Query: 179 LAATARESGAFRREILGISTPNGLV--EQDETIRPGTSVEKLGTLQASFRNDELSARFPQ 236
            AA A E G F+  ++ +   NGLV  ++DE +RPGT ++ L +L  SF+       F  
Sbjct: 176 RAANAWEKGYFKNSVVPVKDQNGLVILDRDEHMRPGTDMQALASLNPSFQMPGEMGGFEA 235

Query: 237 IGWNVT-----------AGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDP 285
           +G               AGN+S I DGA+A+L+ S++  + +GLKPRAR  AF   G DP
Sbjct: 236 VGIQAHPEIERINYVHHAGNSSGIVDGAAAVLIGSKAGGEAMGLKPRARIRAFANIGSDP 295

Query: 286 VMMLTAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIA 345
            +MLT P+  +++ +K++ +KL  ID +E+NEAFA V L + +A      ++N  GGAIA
Sbjct: 296 ALMLTGPVDVTEKLLKRADMKLSDIDLFELNEAFAAVVLRYCQAFDIPHDKINVNGGAIA 355

Query: 346 LGHPLGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
           +GHPLGA+G  ++ T+L  LE       L ++C   GM  ATIIER+
Sbjct: 356 MGHPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTATIIERV 402


Lambda     K      H
   0.318    0.132    0.384 

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: 440
Number of extensions: 20
Number of successful extensions: 4
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: 392
Length of database: 402
Length adjustment: 31
Effective length of query: 361
Effective length of database: 371
Effective search space:   133931
Effective search space used:   133931
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 (21.7 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