GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Phaeobacter inhibens BS107

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate GFF3267 PGA1_c33180 acetyl-CoA acetyltransferase

Query= uniprot:D8ITH5
         (401 letters)



>FitnessBrowser__Phaeo:GFF3267
          Length = 390

 Score =  267 bits (683), Expect = 3e-76
 Identities = 166/400 (41%), Positives = 232/400 (58%), Gaps = 17/400 (4%)

Query: 4   LICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDN 63
           +I  A RTP G + G    V A +L  + IR+ +    G   + V++IL GC   AG+  
Sbjct: 5   VIAGAARTPMGGFQGMYDGVAAAELGGSAIRAALA---GAGATTVDEILMGCVLPAGQ-G 60

Query: 64  RNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAP 123
           +  AR AG  AGL   VP +T+N++CGS + A  MA   I  G+   MIAGG+ESMT AP
Sbjct: 61  QAPARQAGFAAGLGEEVPATTLNKMCGSGMKAAMMAYDQIALGQADTMIAGGMESMTNAP 120

Query: 124 FVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAF 183
           +++ K  +  AR        +   F++ L  A      M   AE+ A  +Q  R  QD +
Sbjct: 121 YLLPKMRNG-ARLG--HGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAETYQFTREAQDEY 177

Query: 184 ALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHP---RPDTTLATLAKLKGV 240
           AL S     AAQ +G F  EIAP+T+  +KG+  V   DE P   RPD     +  LK  
Sbjct: 178 ALTSLSNALAAQESGAFDAEIAPVTVKTRKGET-VTNADEQPKSARPDK----IPTLKPA 232

Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300
            R DGTVTA NAS ++DGA AL+LAS  AA+   L  RAR++G A+   AP +    P P
Sbjct: 233 FRKDGTVTAANASSISDGAAALVLASEDAAEAQGLTVRARIMGHASHAQAPGLFTTAPVP 292

Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360
           A +K++AQ+G T++ +D+ E+NEAFA   +A M ++GLP D   VN NGGA A+GHP+GA
Sbjct: 293 AAKKLMAQLGWTVSDVDLWEVNEAFAVVPMAFMHEMGLPRD--KVNVNGGACALGHPIGA 350

Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           SGAR++ T +N LE+   +  +  +CIG G+G A+ IER+
Sbjct: 351 SGARIMVTLLNALEKRNLKRGIAAICIGGGEGTAIAIERM 390


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: 383
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: 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 17 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