GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Shewanella halifaxensis HAW-EB4

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_012275149.1 SHAL_RS00075 acetyl-CoA C-acyltransferase FadA

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



>NCBI__GCF_000019185.1:WP_012275149.1
          Length = 387

 Score =  296 bits (757), Expect = 9e-85
 Identities = 173/404 (42%), Positives = 241/404 (59%), Gaps = 23/404 (5%)

Query: 1   MRDVFICDAIRTPIGRF-GGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQ 59
           M++  I D IRTP+GR   G    VRA+ L+A  +K+L+E NP +  + +++V +GC  Q
Sbjct: 1   MKNAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKSLLERNPKLDPNTIEDVMWGCVQQ 60

Query: 60  AGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119
             E   N+AR A LLAG+P+ +  VT+NRLC S MDA+  A RAI +G+ +  I GGVE 
Sbjct: 61  TLEQGFNIARNAALLAGIPKQVGAVTVNRLCGSSMDALHQAARAIMTGQGDTFIVGGVEH 120

Query: 120 MSRAPFVMG-KAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSR 178
           M   P   G     G + N+      +G                   TA+ +   + ++R
Sbjct: 121 MGHVPMNHGVDFHPGLANNVAKGSAMMGL------------------TAEMLGKMHGITR 162

Query: 179 ADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKL 237
             QDAFA+RS Q+A AA   G FA EIV +      G  I V+ DE +RPET++E+L+ L
Sbjct: 163 EQQDAFAVRSHQRAHAATVEGRFANEIVAIEGHDADGALIRVDHDEVIRPETSMESLSGL 222

Query: 238 KPVNGP-DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGI 296
           +P   P + TVTAG +S ++DGA+A+++   E  K  GL  RAR+  MA  G    +MG 
Sbjct: 223 RPAFDPANGTVTAGTSSALSDGASAMLVMEEEKAKALGLPIRARIRSMAIAGCDAAIMGY 282

Query: 297 GPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQ-VNPNGGAIALG 355
           GPVPA +K  +R G+ V D DVIELNEAFA+Q L  +++LG+ D   + VN NGGAIALG
Sbjct: 283 GPVPATQKALKRAGLTVDDLDVIELNEAFAAQSLPCVKDLGLMDVVDEKVNLNGGAIALG 342

Query: 356 HPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399
           HPLG SG R+  T ++ +E    + GLATMC+G+GQG+A   ER
Sbjct: 343 HPLGCSGTRISTTLINLMEAKDAKYGLATMCIGLGQGIATIFER 386


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: 398
Number of extensions: 27
Number of successful extensions: 6
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: 387
Length adjustment: 31
Effective length of query: 369
Effective length of database: 356
Effective search space:   131364
Effective search space used:   131364
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