GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Pseudomonas putida KT2440

Align prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); Chorismate mutase (EC 5.4.99.5) (characterized)
to candidate PP_1769 PP_1769 chorismate mutase/Prephenate dehydratase

Query= BRENDA::O30012
         (620 letters)



>FitnessBrowser__Putida:PP_1769
          Length = 367

 Score =  173 bits (438), Expect = 1e-47
 Identities = 120/369 (32%), Positives = 199/369 (53%), Gaps = 24/369 (6%)

Query: 259 ATKKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIK---MERGE-PIELKDVEEEK 314
           A    + ++ LR  I S+D  IL LI  R   A ++AR+K   ++ GE P+  +   E  
Sbjct: 2   ADMSEQELKALRVRIDSLDEKILELISDRARCAEEVARVKTASLKEGEKPVFYRPEREAA 61

Query: 315 LWEVMSKTTLNPV---KLKEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMAL 369
           + + + +    P+   ++  +F  IMS  LA EE  K       IA LGP+G+F++  A+
Sbjct: 62  VLKRVMERNKGPLGNEEMARLFREIMSSCLALEEPLK-------IAYLGPEGTFTQAAAM 114

Query: 370 KLVGSRVPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEA 429
           K  G  V  R  +  DE+ + V +G V++G+VP+ENS  G V   +D+ L HD+ + GE 
Sbjct: 115 KHFGHAVISRPMAAIDEVFREVAAGAVNFGVVPVENSTEGAVSHTLDSFLEHDMVICGEV 174

Query: 430 KLEVNHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML-- 487
           +L ++H L+     +   I  IYSH Q++AQC  +++ + P+V     +S ++AA+ +  
Sbjct: 175 ELRIHHHLLVGENTKTDSITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNAEAAKRVKG 234

Query: 488 DDYSAAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEG-KITSLFFGVED 546
           +  SAAI  + AA  Y L  L + I+D +  N TRF +I  +     G   TS+   + +
Sbjct: 235 EWNSAAIAGDMAANLYGLTRLAEKIED-RPDNSTRFLMIGNQEVPPTGDDKTSIIVSMSN 293

Query: 547 KPGALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEV----EAPLREEDLLDLKQVT 602
           KPGAL ++L  F++ G +L ++E+RP+ +G   YVFF++       PL +  L  + Q  
Sbjct: 294 KPGALHELLVPFYQNGIDLTRIETRPSRSGKWTYVFFIDFVGHHRDPLIKAVLEQISQEA 353

Query: 603 TFYKVVGVF 611
              KV+G +
Sbjct: 354 VALKVLGSY 362


Lambda     K      H
   0.320    0.137    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: 459
Number of extensions: 26
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: 620
Length of database: 367
Length adjustment: 33
Effective length of query: 587
Effective length of database: 334
Effective search space:   196058
Effective search space used:   196058
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: 51 (24.3 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