GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Kocuria flava HO-9041

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_058857241.1 AS188_RS00800 acetyl-CoA C-acetyltransferase

Query= uniprot:D8ITH5
         (401 letters)



>NCBI__GCF_001482365.1:WP_058857241.1
          Length = 396

 Score =  242 bits (618), Expect = 1e-68
 Identities = 154/399 (38%), Positives = 233/399 (58%), Gaps = 10/399 (2%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           + ++    RTP G+  G L +  A +L A  +R  +ER  GV   +V+ +L G   QAG 
Sbjct: 6   DVVVLSGARTPQGKILGQLASFTAAELGAHAVRHALER-AGVAPEQVDYVLMGHVLQAGA 64

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
             +N AR A + AG+P+ VP  TVN++C S L AV  AAR I++GE ++++AGG ESMT 
Sbjct: 65  -GQNPARQAAVTAGIPLDVPAETVNKVCLSGLVAVTHAARMIRAGEAEVVVAGGQESMTS 123

Query: 122 APFV-MGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180
           AP + +G  +        + D       V+  + A   + S+ E+      +  I+RA+Q
Sbjct: 124 APHLALGVRQGKSYGDLKLEDAVAKDGLVD--VAACVSMGSLTESGNG---ERAISRAEQ 178

Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240
           D  A +S +R A A   G F  EIAP+T+PQ+KGDPLVV TD+  RP+ T  ++A+L+  
Sbjct: 179 DEVAAQSHRRAARAAEEGVFREEIAPVTVPQRKGDPLVVDTDQGVRPEATAESMARLRPA 238

Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300
              DGT+TAGN+S ++DGA AL+L++ + A  + L+  A V            +   P+ 
Sbjct: 239 FAQDGTITAGNSSPLSDGAAALVLSTREYAQRHGLEWLAVVGAPGQVAGPDTSLHSQPSR 298

Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360
           A+   +A+ G ++  +D IE+NEAFA+  +  +RDL  P + A+V  +GGA+A+GHP+GA
Sbjct: 299 AIEAAVAKAGWSVQDLDFIEINEAFASVLIQSLRDLDYPLERANV--HGGAVAVGHPIGA 356

Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIER 399
           SGARL   A  +L R G   A  ++C G GQG AL++ R
Sbjct: 357 SGARLALHAAFELARRGTGRAAVSLCGGGGQGEALLLHR 395


Lambda     K      H
   0.320    0.135    0.394 

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: 413
Number of extensions: 20
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: 396
Length adjustment: 31
Effective length of query: 370
Effective length of database: 365
Effective search space:   135050
Effective search space used:   135050
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 24 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