GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc02228
          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 (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