GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ1 in Sinorhizobium meliloti 1021

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate SMc03879 SMc03879 acetyl-CoA acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>lcl|FitnessBrowser__Smeli:SMc03879 SMc03879 acetyl-CoA
           acetyltransferase
          Length = 393

 Score =  305 bits (782), Expect = 1e-87
 Identities = 174/396 (43%), Positives = 243/396 (61%), Gaps = 10/396 (2%)

Query: 6   ICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNR 65
           I    RT +G + GA  +  A +L A  ++ +L R   ++A  +D+VILG    AGE  +
Sbjct: 8   IASAARTAVGSFNGAFGNTLAHELGAAAIKAVLER-AGVEAGEVDEVILGQVLPAGE-GQ 65

Query: 66  NVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPF 125
           N AR A + AGLPQ  +   +N+LCGSGL A+    + I  GD  +++AGG+ESMS AP 
Sbjct: 66  NPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAPH 125

Query: 126 VMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQDSFA 185
                        +M DT I     +       G      TAENVA   +++RE+QD FA
Sbjct: 126 CAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGI-----TAENVARKWQLTREEQDEFA 180

Query: 186 LRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPFRAN 245
           L SQ +   AQ +G  A+EIVP V+K +KG V  +  DE++R   TL+ +  L+  F   
Sbjct: 181 LASQNKAEAAQKAGRFADEIVPFVVKTRKGDVN-VDQDEYIRHGATLDSIAKLRPAFDKE 239

Query: 246 GVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPATRR 305
           G +TAGNASG+NDGAAA ++ +E  AA +G+ P ARIV+ ATAGV+P++MG GP+PA+R+
Sbjct: 240 GTVTAGNASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRK 299

Query: 306 VLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMSGAR 365
            LE+AG S+ D++++E NEAFAAQA  V ++LG   D   VN NGGAIA+GHP+G SGAR
Sbjct: 300 ALEKAGWSVADIELVEANEAFAAQACAVNKDLGW--DPSIVNVNGGAIAIGHPIGASGAR 357

Query: 366 LALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           +      E+ RR     L T+CIG G G+AM +ER+
Sbjct: 358 VLNTLLFEMKRRGVSKGLATLCIGGGMGVAMCVERL 393


Lambda     K      H
   0.319    0.135    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: 446
Number of extensions: 24
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
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: 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, 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