GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Kocuria flava HO-9041

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_058859372.1 AS188_RS14085 thiolase family protein

Query= uniprot:D8ITH5
         (401 letters)



>NCBI__GCF_001482365.1:WP_058859372.1
          Length = 397

 Score =  342 bits (877), Expect = 1e-98
 Identities = 199/401 (49%), Positives = 259/401 (64%), Gaps = 14/401 (3%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +A I DA+RTPFGR+GGAL  VR DDLAA  +   + R PG+D + +++++ G AN AGE
Sbjct: 3   QAYIYDAVRTPFGRFGGALAGVRPDDLAAHVLGEQVGRAPGLDPAAIDEVVLGNANGAGE 62

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
           +NRNVARMA LLAGLP+ +PG+TVNRLCGSSLDA  +A+R I +GE  +++ GGVESM+R
Sbjct: 63  ENRNVARMATLLAGLPVELPGTTVNRLCGSSLDAAIIASRQIGAGEADVVLVGGVESMSR 122

Query: 122 APFVMGKAESAF-ARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180
           AP+V+ K E  + A    +  TT+GWR VN  M+ ++ + S+ E  E +A    I R   
Sbjct: 123 APWVLPKTEKPYPAGDMTLASTTLGWRLVNKRMRPEWTV-SLGEATEQLAERHGITRDRM 181

Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240
           D FA RS Q    A   GF+    A LT+ Q  G  L  T DE  R  +T+  LA LK V
Sbjct: 182 DEFAYRSHQLTQQAWDEGFY----ADLTV-QVPGTEL--TRDESVRASSTVEKLAGLKTV 234

Query: 241 VRPD---GTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFG 297
            RP+   GTVTAGNAS +NDGA A LL S KAA+L  L+P AR+ G   A   P+  GF 
Sbjct: 235 FRPEEQGGTVTAGNASPLNDGASAALLGSEKAAELTGLQPLARIAGRGAAANEPQFFGFA 294

Query: 298 PAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHP 357
           P  A    L + G+T   +  +ELNEAFAAQ LA +   G+  D A VN +GGAIAIGHP
Sbjct: 295 PVEAANSALRRAGITWDDVAAVELNEAFAAQSLACVDAWGI--DPAIVNRHGGAIAIGHP 352

Query: 358 LGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIE 398
           LGASG R++ T    L+ SG R+ +  +CIGVGQG+A+V+E
Sbjct: 353 LGASGTRILGTLARSLQASGQRWGVAAICIGVGQGLAVVLE 393


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: 436
Number of extensions: 15
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: 401
Length of database: 397
Length adjustment: 31
Effective length of query: 370
Effective length of database: 366
Effective search space:   135420
Effective search space used:   135420
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