GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Herbaspirillum seropedicae SmR1

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 HSERO_RS18430 HSERO_RS18430 chorismate mutase

Query= BRENDA::O30012
         (620 letters)



>FitnessBrowser__HerbieS:HSERO_RS18430
          Length = 357

 Score =  167 bits (423), Expect = 7e-46
 Identities = 113/352 (32%), Positives = 185/352 (52%), Gaps = 16/352 (4%)

Query: 269 LRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSKTT--LNP 326
           LR  I +ID+ IL L+ +R   A+++  +K E   P+   + E + L     +    L  
Sbjct: 9   LRQKIDAIDAQILDLLNQRARVAQEVGHVKAETNAPVFRPEREAQVLRRAADRNPGPLLG 68

Query: 327 VKLKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYCSTTDE 386
             ++ IF  +MS  +  E +V      +A LGP+G+FSE+   +  G  +    C + DE
Sbjct: 69  ADIQTIFREVMSACRALEKRVV-----VAYLGPEGTFSEQAVYQQFGHAIEGLSCVSIDE 123

Query: 387 IIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKRKIELK 446
           + +  E+G  D+G+VPIENS  G +   +D LL   + + GE  + V+H L+     +++
Sbjct: 124 VFRDAEAGTADFGVVPIENSSEGVINRTLDLLLQTTLTISGEVSIPVHHSLMTASG-KME 182

Query: 447 EIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSENAARFYR 504
            I  I +H QA+AQC  ++N   PS+  +   S ++AARM   D   AAI  E A + Y 
Sbjct: 183 GITRICAHSQALAQCNAWLNQNYPSIERQAVASNAEAARMAGEDQSVAAIAGEIAGQKYN 242

Query: 505 LHVLRKGIQDLKGRNITRFYLI-RRRSGRSEGKITSLFFGVEDKPGALKDVLEVFHKKGF 563
           L  +   IQD    N TRF +I R R+  S    TS+   V +K GA+ ++L    + G 
Sbjct: 243 LQTVNAHIQD-DPHNRTRFAVIGRLRTAPSGRDQTSIVLSVPNKAGAVYNLLAPLARHGV 301

Query: 564 NLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTFYKVVGVF 611
           ++ + ESRPA  G  +Y F+V++E   ++E     L +L+Q   F+K++G +
Sbjct: 302 SMTRFESRPARMGAWEYYFYVDLEGHEQDEKVAQALEELRQNAAFFKLLGSY 353


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: 397
Number of extensions: 22
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 620
Length of database: 357
Length adjustment: 33
Effective length of query: 587
Effective length of database: 324
Effective search space:   190188
Effective search space used:   190188
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