GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Dinoroseobacter shibae DFL-12

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate 3607238 Dshi_0653 Prephenate dehydratase (RefSeq)

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__Dino:3607238
          Length = 280

 Score =  132 bits (333), Expect = 8e-36
 Identities = 89/273 (32%), Positives = 142/273 (52%), Gaps = 10/273 (3%)

Query: 95  LRVAYLGPEGTFSQAAALKHFGH-SVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEGA 153
           L++A+ G  G +S  A   H       + P    ++VF  V  G+ + G++PVENST G 
Sbjct: 3   LKIAFQGEPGAYSHQAC--HDARPDAEAVPCRTFEDVFAAVHDGSCDLGMLPVENSTYGR 60

Query: 154 VNHTLDSFLEHDIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYP 213
           V        E  + I  E  +R+H +LL     K   I    SH   L QCR +L AH  
Sbjct: 61  VADIHRLLPESGLHIIEEAFVRVHINLLAVPGAKLGDIRTAQSHTVLLGQCRSFLRAH-- 118

Query: 214 NVERVAVSSNADAAKRVKSEWN--SAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIG 271
           +++ V  +  A +A  V  E N   AA+A ++A ++YGL  LA  IED+  N+TRFLI+ 
Sbjct: 119 DIQPVTGADTAGSAMHVAQEGNPAHAALASELAGEIYGLDVLARHIEDQDNNTTRFLIMT 178

Query: 272 SQ-EVPPTGDDK--TSIIVSMRNKPGALHELLMPFHSNGIDLTRIETRPSRSGKWTYVFF 328
            + ++   G  K  TS +  +RN P AL++ +  F +NG+++T++E+           F+
Sbjct: 179 PELDLTRRGSGKMITSFVFQVRNIPAALYKAMGGFATNGVNMTKLESYMVGGSFTATQFY 238

Query: 329 IDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361
            D  GH  D  ++  L+++G+    L++LG YP
Sbjct: 239 ADIEGHPDDANVRRALDELGYFTSQLEILGVYP 271


Lambda     K      H
   0.319    0.133    0.390 

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: 200
Number of extensions: 9
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: 365
Length of database: 280
Length adjustment: 28
Effective length of query: 337
Effective length of database: 252
Effective search space:    84924
Effective search space used:    84924
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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