GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Novosphingobium fuchskuhlense FNE08-7

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_067908804.1 AQZ52_RS09260 acetyl-CoA C-acyltransferase

Query= uniprot:D8ITH5
         (401 letters)



>NCBI__GCF_001519075.1:WP_067908804.1
          Length = 398

 Score =  258 bits (658), Expect = 3e-73
 Identities = 157/400 (39%), Positives = 230/400 (57%), Gaps = 15/400 (3%)

Query: 4   LICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDN 63
           +I    RTP G   G+L  V A  L A  +++ +ER  G+   +VE I  GC   AG   
Sbjct: 11  VILSFARTPMGAMQGSLADVSATQLGATAVKAAVER-AGIAGEKVERIYMGCVLPAGL-G 68

Query: 64  RNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAP 123
           +  AR A + AGLP +V  +TV ++CGS + A+ M A A+ SG + +++AGG+ESMT AP
Sbjct: 69  QAPARQAAIYAGLPASVEATTVGKVCGSGMQAMIMGAEALASGSIDMVVAGGMESMTNAP 128

Query: 124 FVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAF 183
           +++ K  S  AR     DT     F++ L  A     +M   A++ A  +Q+ R  QDA+
Sbjct: 129 YLLKKHRSG-ARIG--HDTAYDHMFLDGLEDAYEPGRAMGTFAQDTANAYQLTREQQDAY 185

Query: 184 ALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHP---RPDTTLATLAKLKGV 240
           A+ S +R   A A G FA EI P+T+  + G+  +V TDE P   +PD   A    LK  
Sbjct: 186 AIESLRRAQTAIAEGAFAAEITPVTVASRAGET-IVDTDEAPGKGKPDKIPA----LKPA 240

Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300
              DGT+TA  +S ++DGA A++L     A    LKP ARV+ +A    AP+     P  
Sbjct: 241 FAKDGTITAATSSSISDGAAAMVLTRESVAAADGLKPVARVVALAAHAQAPKDFTTAPVG 300

Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360
           A+ K+L + G ++A +D+ E+NEAFA   +  M DLG+P +   +N +GGA A+GHP+GA
Sbjct: 301 AITKLLGKAGWSIADVDLFEVNEAFACVAMFAMHDLGIPHE--KINVHGGATALGHPIGA 358

Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           SGAR+VTT I  L+R G +  + ++CIG G+  A+ IE V
Sbjct: 359 SGARIVTTLIGALQRHGKKRGVASLCIGGGEATAVAIELV 398


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: 411
Number of extensions: 24
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: 398
Length adjustment: 31
Effective length of query: 370
Effective length of database: 367
Effective search space:   135790
Effective search space used:   135790
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