GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Burkholderia phytofirmans PsJN

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BPHYT_RS17350 BPHYT_RS17350 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__BFirm:BPHYT_RS17350
          Length = 263

 Score =  152 bits (384), Expect = 7e-42
 Identities = 93/264 (35%), Positives = 147/264 (55%), Gaps = 7/264 (2%)

Query: 1   MAYENIL--VETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSE 58
           M+YE I   ++    V  +TLNRP  LN+   A+  EL AAL + +   A  A+V+TG+ 
Sbjct: 1   MSYEAIRLDIDASSHVATITLNRPDKLNSFTRAMHQELSAALDQVETSGA-RALVLTGAG 59

Query: 59  KAFAAGADIGMMSTYTYMDVYKGDYITRNWETV----RSIRKPIIAAVAGFALGGGCELA 114
           + F AG D+  +          G+ I +++  +    +++  P+IAAV G A G G  LA
Sbjct: 60  RGFCAGQDLADLDFTPGAMTDLGELIEQHFNPLIRRLQALPLPVIAAVNGTAAGAGANLA 119

Query: 115 MMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERA 174
           + CD++ AA +A F Q  +K+G++P +GGT  LP+ V  A+A+ L +T   + A +AE  
Sbjct: 120 LACDLVLAARSASFIQAFVKIGLVPDSGGTWFLPQRVGMARALGLAITGDKLSAEKAESW 179

Query: 175 GLVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSL 234
           GL+ + +  A L + A   AA +A+ P+ A+  +K ++      TL + +  ER L   L
Sbjct: 180 GLIWQAVDDAELAETAAKLAAQLAQQPTRAIAAIKRAMRAGATQTLDQQLDLERDLQREL 239

Query: 235 FATEDQKEGMAAFVEKRKPVFKHR 258
            A+ D  EG+ AFVEKR P F+ R
Sbjct: 240 GASHDYAEGVQAFVEKRAPRFEGR 263


Lambda     K      H
   0.321    0.134    0.380 

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: 157
Number of extensions: 6
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: 258
Length of database: 263
Length adjustment: 25
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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