GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Echinicola vietnamensis KMM 6221, DSM 17526

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Echvi_4069 Echvi_4069 Enoyl-CoA hydratase/carnithine racemase

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



>FitnessBrowser__Cola:Echvi_4069
          Length = 261

 Score =  165 bits (418), Expect = 8e-46
 Identities = 102/255 (40%), Positives = 141/255 (55%), Gaps = 4/255 (1%)

Query: 5   NILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFAA 63
           NIL E +  +  +T+NR   LNA+N   ++EL     E   + +I  +V+TGS EKAF A
Sbjct: 6   NILSENKDGILYLTINRESKLNAINFDTLEELKNIFNEVSDNKSIRGVVLTGSGEKAFVA 65

Query: 64  GADIGMMSTYTYMDVYK-GDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFA 122
           GADI  ++    ++  K  +     +  + S  KP+IA V GFALGGGCEL+M C +  A
Sbjct: 66  GADISEIAELNELNARKFSENGQEVFSLIESCHKPVIAVVNGFALGGGCELSMACHMRIA 125

Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182
              AKFGQPE+ LGI+PG GGTQRL   + + KA +L +T   +DAAEA+  GLV+ V  
Sbjct: 126 TSNAKFGQPEVNLGIIPGYGGTQRLTFLIGRTKANELLMTGDMVDAAEAKALGLVNYVTQ 185

Query: 183 A-ASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQK 241
             A  + +A      I      ++ M+ + VN  Y      G   E   F     +ED  
Sbjct: 186 TKAEAIQKAEEILQKIMTKAPLSIGMIIDCVNAVYSND-ENGYLIEANSFARCVKSEDYS 244

Query: 242 EGMAAFVEKRKPVFK 256
           EG +AF+EKRKP FK
Sbjct: 245 EGTSAFLEKRKPNFK 259


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: 149
Number of extensions: 5
Number of successful extensions: 4
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: 261
Length adjustment: 24
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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