GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Burkholderia phytofirmans PsJN

Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate BPHYT_RS17345 BPHYT_RS17345 acetyl-CoA acetyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411
         (393 letters)



>FitnessBrowser__BFirm:BPHYT_RS17345
          Length = 400

 Score =  313 bits (801), Expect = 7e-90
 Identities = 178/399 (44%), Positives = 248/399 (62%), Gaps = 11/399 (2%)

Query: 5   EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALER-AAVDPALVGHLVMGNVIPTET 63
           + ++  A RT IG +GG+LKDV   DL    +KA +ER   VD   V  ++ G       
Sbjct: 3   DAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQAGE 62

Query: 64  RDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSR 123
            +  ++R++A+ AG+P E P   +NRLCGSG+ A+  AA+ +  G+A +++  G ESM+R
Sbjct: 63  DNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESMTR 122

Query: 124 GPYLMPAARWGSRMGNAQVIDYMLG------ILHDPFHGIHMGITAENVAARNGITREMQ 177
            P++M  A   +    A + D  +G      ++   +    M  TAENVAA   ++R  Q
Sbjct: 123 APFVMGKAT-SAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRADQ 181

Query: 178 DALAFEDQQRAAHAIANGYFSEQIATVEIQDRKGVKLFSV-DEHPRATSLEQLAAMKPAF 236
           DA A   QQ+AA A  +G  +++I  VEI  +KG  + ++ DEHPR TSLE L  +K   
Sbjct: 182 DAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKGVV 241

Query: 237 KKDGSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPA 296
           + DGSVTAGNASG+NDGA AL++A+  A     L+  AR+V  A AGVEP  MG+GP PA
Sbjct: 242 RPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAPA 301

Query: 297 TRLALKRAGLTVADLDVIEANIAFAAQACAVSQELDL--DPAKVNPNGSGIALGHPVGAT 354
           T+  LK+ G+T+  LDVIE N AFA+Q  AV + L L  D  +VNPNG  IALGHP+GA+
Sbjct: 302 TQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLGAS 361

Query: 355 GAIIATKAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393
           GA + T A+++L RT GR+AL TMCIG GQGIA + ER+
Sbjct: 362 GARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400


Lambda     K      H
   0.318    0.133    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: 384
Number of extensions: 18
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: 393
Length of database: 400
Length adjustment: 31
Effective length of query: 362
Effective length of database: 369
Effective search space:   133578
Effective search space used:   133578
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 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