GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Pseudomonas fluorescens FW300-N2E3

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 AO353_02070 AO353_02070 prephenate dehydratase

Query= BRENDA::O30012
         (620 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_02070
          Length = 364

 Score =  171 bits (433), Expect = 5e-47
 Identities = 118/364 (32%), Positives = 198/364 (54%), Gaps = 24/364 (6%)

Query: 264 ESIEELRGLIKSIDSLILRLIERRIDAARQIARIKME---RGE-PIELKDVEEEKLWEVM 319
           + ++ LR  I ++D  IL LI  R   A+++AR+KM     GE P+  +   E ++ + +
Sbjct: 4   QELKALRLRIDALDEKILELISERARCAQEVARVKMATLAEGEVPVFYRPEREAQVLKRV 63

Query: 320 SKTTLNPV---KLKEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGS 374
            +    P+   ++  +F  IMS  LA E+  KVA        LGP+G+F++  A+K  G 
Sbjct: 64  MERNQGPLGNEEMARLFREIMSSCLALEQPLKVA-------YLGPEGTFTQAAAMKHFGH 116

Query: 375 RVPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVN 434
            V  +  +  DE+ + V +G V++G+VP+ENS  G V   +D+ L HD+ + GE +L ++
Sbjct: 117 AVISKPMAAIDEVFREVAAGAVNFGVVPVENSTEGAVNHTLDSFLEHDMVICGEVELRIH 176

Query: 435 HCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSA 492
           H L+     +   I  IYSH Q++AQC  +++ + P+V     +S ++AA+ +  +  SA
Sbjct: 177 HHLLVGENTKTDSISRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNAEAAKRVKGEWNSA 236

Query: 493 AIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEG-KITSLFFGVEDKPGAL 551
           AI  + AA  Y L  L + I+D +  N TRF +I  +     G   TS+   + +KPGAL
Sbjct: 237 AIAGDMAAGLYGLTRLAEKIED-RPDNSTRFLMIGSQEVPPTGDDKTSIIVSMSNKPGAL 295

Query: 552 KDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEV----EAPLREEDLLDLKQVTTFYKV 607
            ++L  FH  G +L ++E+RP+ +G   YVFF++       PL +  L  + Q     KV
Sbjct: 296 HELLVPFHDNGIDLTRIETRPSRSGKWTYVFFIDFVGHHRDPLIKAVLEKISQEAVALKV 355

Query: 608 VGVF 611
           +G +
Sbjct: 356 LGSY 359


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: 444
Number of extensions: 26
Number of successful extensions: 2
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: 364
Length adjustment: 33
Effective length of query: 587
Effective length of database: 331
Effective search space:   194297
Effective search space used:   194297
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