GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Sphingopyxis indica DS15

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_089214379.1 CHB69_RS02585 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_900188185.1:WP_089214379.1
          Length = 395

 Score =  260 bits (664), Expect = 6e-74
 Identities = 143/390 (36%), Positives = 228/390 (58%), Gaps = 8/390 (2%)

Query: 11  RTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGEDNRNVARM 70
           RTP+G   G L+   A DL A  +KA +E    V+ + V+ ++ GC   AG   +  AR 
Sbjct: 14  RTPMGGMQGVLSDASATDLGATAVKAAVE-RAGVKGEDVERIYMGCVLPAGL-GQAPARQ 71

Query: 71  ALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAPFVMGKA 130
           A + AGLP+S+   T+N++C SGM  +     A+A+G ++LA+AGG+ESM+ AP+++ K 
Sbjct: 72  AAIKAGLPKSVQATTVNKVCGSGMQTVIMGAEALAAGSIDLAVAGGMESMTNAPYLLKKH 131

Query: 131 ESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDAFALRSQQ 190
            SG        DT     F++ L  +     +M   A + AD YQ+SR  QD +A+ S +
Sbjct: 132 RSGARIG---HDTAYDHMFLDGLEDAYDAGRAMGTFAQDTADAYQLSRQAQDDYAIESLR 188

Query: 191 KAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPVNGPDKTVTAG 250
           +A AA A G FA EI PV +  +KGE +V+ DE    +   + +  L+P    D T+TA 
Sbjct: 189 RAQAAIADGAFAAEITPVTLTTRKGEVVVDTDEQ-PGKGNPDKIPTLRPAFAKDGTITAA 247

Query: 251 NASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVRKLTERLG 310
            +S ++DGAAA++L      +K G  P A+++  A+    P+   + P+ A+ K+  + G
Sbjct: 248 TSSSISDGAAAVVLTRQSVAEKKGAKPVAKLVAHAAHAQEPKDFTVAPIGAINKVLAKAG 307

Query: 311 VAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGARLVLTAL 370
            ++ D D+ E+NEAFA   +  + +LG+  D  ++N NGGA ALGHP+G SG R++ T +
Sbjct: 308 WSIGDVDLFEVNEAFACVAMFAMHDLGIPHD--RINVNGGATALGHPIGASGTRIIATLI 365

Query: 371 HQLEKSGGRKGLATMCVGVGQGLALAIERV 400
             L+  G ++G+A++C+G G+  A+AIE V
Sbjct: 366 AALQNRGKKRGIASLCIGGGEATAVAIELV 395


Lambda     K      H
   0.318    0.134    0.383 

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: 369
Number of extensions: 17
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: 400
Length of database: 395
Length adjustment: 31
Effective length of query: 369
Effective length of database: 364
Effective search space:   134316
Effective search space used:   134316
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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