GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Shewanella amazonensis SB2B

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 6935813 Sama_0031 3-ketoacyl-CoA thiolase (RefSeq)

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



>FitnessBrowser__SB2B:6935813
          Length = 387

 Score =  235 bits (600), Expect = 1e-66
 Identities = 156/399 (39%), Positives = 217/399 (54%), Gaps = 17/399 (4%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59
           M +AVIV   RTP+G++  G        TL    ++  + R  G+DP  +EDV+ G   Q
Sbjct: 1   MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ 60

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
               G NIAR A L AG+P T    T++R C S ++A+  A+R+++    +  + GG E 
Sbjct: 61  TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH 120

Query: 120 ISLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179
           +  V  +    FH   P L A        M  TAE + K +GISRE QD++++ S +R  
Sbjct: 121 MGHVPMNHGVDFH---PGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAH 177

Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239
           AA   G+F +EI  I         A GA+    I +  DE  RPETT E LAGL+ V   
Sbjct: 178 AASIEGRFANEIYAIEGH-----DANGAL----IKVDYDEVIRPETTLESLAGLRPVFDP 228

Query: 240 GF-TITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAV 298
              T+TAG +S LSDGA+A ++M ++ A A GL      R M   GC+   MG GPV A 
Sbjct: 229 ANGTVTAGTSSALSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPAT 288

Query: 299 PRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLG---IDPEKLNVNGGAISVGHPYGMS 355
            + L R GLS+ D+ + ELNEAFA Q L C   LG   +  +K+N+NGGAI++GHP G S
Sbjct: 289 QKALARAGLSIQDMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCS 348

Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           GAR++   +     + A   + TMC+G G G A +FE V
Sbjct: 349 GARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 387


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: 392
Number of extensions: 23
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: 395
Length of database: 387
Length adjustment: 31
Effective length of query: 364
Effective length of database: 356
Effective search space:   129584
Effective search space used:   129584
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.

Links

Downloads

Related tools

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