GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Burkholderia phytofirmans PsJN

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BPHYT_RS03230 BPHYT_RS03230 acetyl-CoA acetyltransferase

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



>FitnessBrowser__BFirm:BPHYT_RS03230
          Length = 399

 Score =  308 bits (789), Expect = 2e-88
 Identities = 184/395 (46%), Positives = 240/395 (60%), Gaps = 5/395 (1%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQ 59
           + +A IV+ +RTPIGKA RG    T    LL HAI+ AV +  G+D K +ED ++G A+ 
Sbjct: 5   LQDAYIVAASRTPIGKAPRGMFKNTRPDELLVHAIKSAVAQVPGLDTKVIEDAIIGCAIP 64

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
           +   G N+AR   L AGLP +  G T++R CASGL A+A+AA  +     +  + GG ES
Sbjct: 65  EAEQGLNVARMGALLAGLPNSVGGVTVNRFCASGLTALAMAADRIRVGESDAMIAGGCES 124

Query: 120 ISLVQNDKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYSLESQRR 177
           +S+V    M    ++ P +     DV +A  M  TAE VA+R+ ISRE QD +S+ES RR
Sbjct: 125 MSMVP--MMGNKPSMSPHIFDRNEDVGIAYGMGLTAEKVAERWKISREAQDAFSVESHRR 182

Query: 178 TAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVR 237
             AAQQ G+FNDEIA  +      D ATG V  K   +S DEGPR ET+ EGLA L+AV 
Sbjct: 183 AIAAQQAGEFNDEIAAYTITERFPDLATGEVRVKTREVSLDEGPRAETSLEGLAKLRAVF 242

Query: 238 GEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFA 297
               ++TAGN+SQ SDGA A +++S+K      L PL  F      G  P+ MGIGP  A
Sbjct: 243 ANKGSVTAGNSSQTSDGAGALIVVSEKMLKEFNLTPLARFVSFAVRGVPPEIMGIGPKEA 302

Query: 298 VPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGA 357
           +P  LK  GL +DD+   ELNEAFA Q L     LG+DP K+N  GGAI++GHP G +GA
Sbjct: 303 IPAALKAAGLKIDDLDWIELNEAFAAQSLAVIQDLGLDPAKINPLGGAIALGHPLGATGA 362

Query: 358 RLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
             A   +   RRR  KY +VTMCVG GMG+AG+ E
Sbjct: 363 IRASTVVHGLRRRNYKYGMVTMCVGTGMGAAGIIE 397


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: 422
Number of extensions: 14
Number of successful extensions: 3
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: 399
Length adjustment: 31
Effective length of query: 364
Effective length of database: 368
Effective search space:   133952
Effective search space used:   133952
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