GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_068168283.1 HTA01S_RS06660 acetyl-CoA C-acetyltransferase

Query= uniprot:D8ITH5
         (401 letters)



>NCBI__GCF_001592305.1:WP_068168283.1
          Length = 392

 Score =  282 bits (722), Expect = 1e-80
 Identities = 170/399 (42%), Positives = 239/399 (59%), Gaps = 10/399 (2%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           + +I  A RT  G++GG+L    A +L +  I+ L+ R  G+    V +++ G    AG 
Sbjct: 3   DIVIVSAARTAVGKFGGSLAKTPATELGSIVIKELLART-GLPVDAVGEVIMGQVLAAG- 60

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
             +N AR A + AG+    P  T+N +CGS L AV +AA+A+  G+ +++IAGG E+M+ 
Sbjct: 61  CGQNPARQAMMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSEIVIAGGQENMSA 120

Query: 122 APFVM-GKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180
           +P V+ G  +        + DT I    V+ L    Y    M  TAENVA    I R  Q
Sbjct: 121 SPHVLNGSRDGQRMGDWKMTDTMI----VDGLWDV-YNQYHMGITAENVAKAQGITREMQ 175

Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240
           DA A  SQQ+ AAAQAAG F  EI  ++IPQ+KGDP++  +DE     TT   LA L+  
Sbjct: 176 DALAAGSQQKAAAAQAAGKFKDEIVGVSIPQRKGDPVLFNSDEFINAKTTAEVLAGLRPA 235

Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300
               G+VTAGNASG+NDGA A+++ + K A    L P AR+    T+G+ P +MG GP P
Sbjct: 236 FDKSGSVTAGNASGINDGAAAVMVMTAKKAAALGLTPLARIAAFGTSGLDPALMGMGPVP 295

Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360
           A +K LA+ G   + +DV ELNEAFAAQ  AV  ++ L  D A VN NGGAIAIGHP+GA
Sbjct: 296 ASQKALARAGWKASDVDVFELNEAFAAQACAV--NMALDIDPAKVNVNGGAIAIGHPIGA 353

Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIER 399
           SG R++ T +++++R G +  L  +CIG G G++L +ER
Sbjct: 354 SGCRILVTLLHEMQRRGAKKGLAALCIGGGMGVSLAVER 392


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: 403
Number of extensions: 13
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: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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