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_058857811.1 AS188_RS04280 thiolase family protein

Query= uniprot:D8ITH5
         (401 letters)



>NCBI__GCF_001482365.1:WP_058857811.1
          Length = 390

 Score =  216 bits (549), Expect = 1e-60
 Identities = 159/396 (40%), Positives = 204/396 (51%), Gaps = 28/396 (7%)

Query: 10  RTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDNRNVARM 69
           RTP  R G AL  V    L A  + +L+E   G+   +V D++ G A  AG    N AR+
Sbjct: 18  RTPLARAGTALAGVPVHRLLAPVLDALLEET-GLAPEQVADVVVGNAVGAGG---NPARL 73

Query: 70  AGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAPFVMGKA 129
           A L AGLP +VPG TV+R CGS LDAV +A    ++G  +  +AGG ES++ AP    + 
Sbjct: 74  AALEAGLPQSVPGLTVDRQCGSGLDAVVLACHLARAGAGRAFLAGGAESISTAPLRGRRQ 133

Query: 130 ES---AFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAFALR 186
           E    AF R A      +G    +P          M E AE VA +  I R  QDAFALR
Sbjct: 134 EDGGVAFYRRAQFAPEHLG----DP---------DMGEAAETVAREHGIGRERQDAFALR 180

Query: 187 SQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVVRPDGT 246
           S +R  AA AAG FAGE+ P+  P+       VT D  PRP    A LA+   V    GT
Sbjct: 181 SHRRALAAAAAGAFAGELVPVRTPRG-----AVTADNGPRPRLDAALLARFPPVFAAGGT 235

Query: 247 VTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPAVRKVL 306
           VTAGN+ G  DGA A+L+A P AA            G AT GV P  +G G A A R++L
Sbjct: 236 VTAGNSCGDADGAAAVLVADPAAARELGTATALAFRGAATVGVDPARLGLGAAVAARRLL 295

Query: 307 AQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGASGA-RL 365
           A+  + +  +   E NEAFA Q LA    LGL ++   +N  GGA+A+GH  GASGA  +
Sbjct: 296 AEQAVPVRALAAAEFNEAFAGQVLACTDLLGLDEEV--LNAEGGALALGHAYGASGAVSV 353

Query: 366 VTTAINQLERSGGRYALCTMCIGVGQGIALVIERVA 401
           V       E   G   L  +    G G A + E+VA
Sbjct: 354 VRLLARARELPEGSLLLAMISSAGGIGTAALFEKVA 389


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: 438
Number of extensions: 21
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: 390
Length adjustment: 31
Effective length of query: 370
Effective length of database: 359
Effective search space:   132830
Effective search space used:   132830
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.

Links

Downloads

Related tools

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