GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Marinobacter adhaerens HP15

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 GFF1395 HP15_1362 chorismate mutase / prephenate dehydratase

Query= BRENDA::O30012
         (620 letters)



>FitnessBrowser__Marino:GFF1395
          Length = 365

 Score =  158 bits (400), Expect = 3e-43
 Identities = 105/337 (31%), Positives = 175/337 (51%), Gaps = 15/337 (4%)

Query: 268 ELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSKTT---- 323
           ELR  I  +D  I+ LI  R   A+++A +KM      ++     E+  +V+ +      
Sbjct: 10  ELRDEIDQLDQKIMELISARAACAQEVAHVKMTANPGQDVFFYRPEREAQVLRRIKEQNP 69

Query: 324 --LNPVKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYC 381
             L+  ++  +F  IMS     E  +      IA LGP G+F++  ALK  G  V     
Sbjct: 70  GPLSGEEMARLFREIMSACLALEKPMH-----IAFLGPIGTFTQAAALKHFGHSVVSVPL 124

Query: 382 STTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKR 441
              D + + VESG   YG+VP+ENS  G +   +D  ++  +++ GE +L ++H L+   
Sbjct: 125 PAIDAVFREVESGAAHYGVVPVENSTEGMINHTLDMFMSSPLKICGEVQLRIHHHLLVSP 184

Query: 442 KIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSENA 499
           K   +EI  IYSH Q+ AQC  +++ +   +     +S ++AAR    +  +AAI  + A
Sbjct: 185 KHGDQEITRIYSHQQSFAQCRQWLDTHRYGIERVTVSSNAEAARRAAEEPGTAAIAGDMA 244

Query: 500 ARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEG-KITSLFFGVEDKPGALKDVLEVF 558
           A  Y L  L   I+D +  N TRF +I R    + G   +S+   + +KPGAL  +LE F
Sbjct: 245 AELYGLQKLANSIED-RPDNTTRFLIIGREEVPASGHDKSSILVSMRNKPGALYQLLEPF 303

Query: 559 HKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREEDL 595
           H+ G +L ++E+RP+ +G   YVF+++ E  + +E +
Sbjct: 304 HRHGLSLTRIETRPSPSGTWAYVFYIDFEGHMEDEQV 340


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: 466
Number of extensions: 30
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: 620
Length of database: 365
Length adjustment: 33
Effective length of query: 587
Effective length of database: 332
Effective search space:   194884
Effective search space used:   194884
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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