GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Pseudarthrobacter sulfonivorans Ar51

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_058931411.1 AU252_RS15005 thiolase family protein

Query= metacyc::MONOMER-20679
         (395 letters)



>NCBI__GCF_001484605.1:WP_058931411.1
          Length = 403

 Score =  275 bits (703), Expect = 2e-78
 Identities = 171/414 (41%), Positives = 230/414 (55%), Gaps = 31/414 (7%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M EA +V   RTP+G+ Y GAL+A     L    I  AV RAG+DP  +E+V++G A   
Sbjct: 1   MVEAFLVGGVRTPVGR-YGGALSAVRPDDLAALVIREAVSRAGLDPDSIEEVILGNANGA 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G    N+AR A+L AGLP+   G T++R CASGL AI  A+  +     ++ + GG ES+
Sbjct: 60  GEENRNVARMAVLLAGLPLHIPGITVNRLCASGLSAIIQASHMIKSGAADVVIAGGVESM 119

Query: 121 SLVQ--NDKMNTFHA--------------VDPALE----AIKGDVYMAMLDTAETVAKRY 160
           S      +K  T  A              V+P  +    A  G +  +M +TAE VA+  
Sbjct: 120 SRAPWAQEKPATAFAKPGQIFDTSIGWRFVNPLFQKGGLARDGKMTYSMPETAEEVARVD 179

Query: 161 GISRERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEG 220
           GI+RE  D +++ S  R+ AA   G+F DEI P++ K    +            +  DEG
Sbjct: 180 GITREDADAFAVRSHERSLAAIAAGRFRDEIVPVTVKSRKAETV----------VDTDEG 229

Query: 221 PRPETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGM 280
           PR  TT E LAGL+ V   G  +TAGN+S L+DGASA ++ S+   A  GL P       
Sbjct: 230 PRAGTTLEVLAGLRPVVPGGSVVTAGNSSTLNDGASAIIVASEAAIARLGLTPRARIIDG 289

Query: 281 VSYGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLN 340
            S GCEP+ MGIGPV A  ++L R GLS  D+G  ELNEAFA Q L    +LG+DP+ +N
Sbjct: 290 ASAGCEPEIMGIGPVPATQKVLARSGLSASDLGAVELNEAFATQSLASMRRLGLDPDTVN 349

Query: 341 VNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
            +GGAIS+GHP G SG+R+A   L    R  A+  + TMCVG G G+A L E V
Sbjct: 350 NDGGAISLGHPLGSSGSRIAITLLGRMEREDARIGLATMCVGVGQGTAMLLERV 403


Lambda     K      H
   0.316    0.134    0.378 

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: 433
Number of extensions: 21
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: 395
Length of database: 403
Length adjustment: 31
Effective length of query: 364
Effective length of database: 372
Effective search space:   135408
Effective search space used:   135408
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 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