GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Sinorhizobium fredii NGR234

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_012709751.1 NGR_RS27475 acetyl-CoA C-acetyltransferase

Query= SwissProt::P0C7L2
         (401 letters)



>NCBI__GCF_000018545.1:WP_012709751.1
          Length = 393

 Score =  312 bits (800), Expect = 9e-90
 Identities = 177/396 (44%), Positives = 245/396 (61%), Gaps = 10/396 (2%)

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

Query: 66  NVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPF 125
           N AR A + AG+PQ  +   +N+LCGSGL A+    + I  GD  +++AGG+ESMS AP 
Sbjct: 66  NPARQAAIKAGVPQEKTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMAPH 125

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

Query: 186 LRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPFRAN 245
           LRSQ +   AQ +G  A+EIVP ++K +KG VT +  DE++R   TLE +  L+  F   
Sbjct: 181 LRSQNKAEAAQKAGRFADEIVPFIVKTRKGDVT-VDQDEYIRHGATLESIAKLRPAFDKE 239

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

Query: 306 VLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMSGAR 365
            LE+AG  I D++++E NEAFAAQA  V ++LG   D   VN NGGAIA+GHP+G SGAR
Sbjct: 300 ALEKAGWPIGDVELVEANEAFAAQACAVNKDLGW--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: 450
Number of extensions: 20
Number of successful extensions: 6
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 Apr 09 2024. 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