GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Shewanella loihica PV-4

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 5209189 Shew_1667 acetyl-CoA acetyltransferase (RefSeq)

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



>FitnessBrowser__PV4:5209189
          Length = 396

 Score =  198 bits (504), Expect = 2e-55
 Identities = 131/404 (32%), Positives = 210/404 (51%), Gaps = 29/404 (7%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGA 62
           E VIV+  RTP+G  ++G+L++    TL   AI+  +  AG+   +V +V+MG  +  G 
Sbjct: 9   EIVIVAAKRTPMG-GFQGSLSSVPSPTLAATAIKGLMDAAGVQGGDVNEVLMGCVLPAGL 67

Query: 63  TGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISL 122
            G   AR+A L A LP++   TT+++ C SG++ + LA   +     ++ + GG ES+S 
Sbjct: 68  -GQAPARQATLGADLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSADVVIAGGMESMSQ 126

Query: 123 VQ-------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDE 169
                          + K+     +D   +A  G    AM   A+  A  +GI+RE  D 
Sbjct: 127 APYLLDKARGGMRMGHGKVLDHMFLDGLEDAYTGG---AMGTFAQKTADDFGITREAMDN 183

Query: 170 YSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEG 229
           ++L S ++  AA + G F  EI P+          T A    D+ +  DE P      E 
Sbjct: 184 FALSSLQKANAAIESGAFKAEIVPV----------TVASRKGDLVVDTDEQPG-NARPEK 232

Query: 230 LAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDE 289
           +  L+    +  TITA N+S +SDGA+  ++MS   A+ +GL+ L   +G  ++  EP  
Sbjct: 233 IPTLRPAFAKDGTITAANSSSISDGAAVLMMMSADEASKRGLEVLATIKGHTTHSQEPSM 292

Query: 290 MGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVG 349
               PV A+ +LL +   S D++ L+E+NEAFA+  +    +LG+D  K+NVNGGA ++G
Sbjct: 293 FTTAPVGAMNKLLDKVNWSKDEVDLFEINEAFAMVTMLAISELGLDEAKVNVNGGACALG 352

Query: 350 HPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393
           HP G SGAR+    +   + R  K  V ++C+GGG  +A   E+
Sbjct: 353 HPIGCSGARVLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 396


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: 427
Number of extensions: 31
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 395
Length of database: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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