GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Marinobacter adhaerens HP15

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF1551 HP15_1513 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__Marino:GFF1551
          Length = 374

 Score =  239 bits (610), Expect = 1e-67
 Identities = 156/384 (40%), Positives = 212/384 (55%), Gaps = 17/384 (4%)

Query: 14  IGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQGATGGNIARKAL 72
           +G+A  G        TL  + IE   +R   +DPKEVEDV+ G   Q    G N+AR+  
Sbjct: 1   MGRAKNGCFRNVRAETLSANLIEALFERNPKLDPKEVEDVIWGCVNQTKEQGFNVARQIS 60

Query: 73  LRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQNDKMNTFH 132
           L   +P  +A  T++R C S + AI  AA++++    ++   GG E +  V    M    
Sbjct: 61  LLTRIPHESAAQTVNRLCGSAMSAIHTAAQAIMTGNGDVFFVGGVEHMGHVP---MTEGF 117

Query: 133 AVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAAAQQGGKFNDEIA 192
             +PA           M  TAE +AK +GI+RE+QDE+   S R    A   G+F +EI 
Sbjct: 118 DHNPAASKYSAKASNMMGLTAEMLAKMHGITREQQDEFGARSHRLAHEATLEGRFKNEIV 177

Query: 193 PISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AVRGEGFTITAGNASQL 251
           PI        +      FK + + +DE  RPETTAE L+ LK A   +  T+TAG +SQL
Sbjct: 178 PI--------EGHDENGFK-VLIEEDETIRPETTAESLSQLKPAFDPKNGTVTAGTSSQL 228

Query: 252 SDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPRLLKRHGLSVDD 311
           +DGA+A V+MS + A A GLKP+   R M   GC+P  MG GPV A  + LKR GL V+D
Sbjct: 229 TDGAAAMVLMSAERAEALGLKPIAKIRSMAVAGCDPAIMGYGPVPATKKALKRAGLKVED 288

Query: 312 IGLWELNEAFAVQ---VLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLAGHALIEGR 368
           I  WELNEAFA Q   VL     LG+  EK+N+NGGAI++GHP G SGAR++   L   +
Sbjct: 289 IDFWELNEAFAGQSLPVLKDLKLLGVMEEKVNLNGGAIALGHPLGCSGARISTTLLNVMQ 348

Query: 369 RRKAKYAVVTMCVGGGMGSAGLFE 392
            +  K  V TMC+G G G A ++E
Sbjct: 349 AKGGKLGVSTMCIGLGQGIATVWE 372


Lambda     K      H
   0.316    0.134    0.378 

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: 386
Number of extensions: 17
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: 395
Length of database: 374
Length adjustment: 30
Effective length of query: 365
Effective length of database: 344
Effective search space:   125560
Effective search space used:   125560
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 (21.6 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