GapMind for Amino acid biosynthesis

 

Aligments for a candidate for pre-dehydr in Shewanella amazonensis SB2B

Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 6936707 Sama_0894 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)

Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER
         (373 letters)



>lcl|FitnessBrowser__SB2B:6936707 Sama_0894 bifunctional chorismate
           mutase/prephenate dehydrogenase (RefSeq)
          Length = 379

 Score =  427 bits (1098), Expect = e-124
 Identities = 216/371 (58%), Positives = 269/371 (72%), Gaps = 1/371 (0%)

Query: 3   AELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAE 62
           AEL  LR  ID VD  LL+LL KRL+LVA+VG VK   GLPIY P REA+ML  RRAEAE
Sbjct: 7   AELENLRGLIDGVDSQLLSLLRKRLDLVAQVGTVKHAAGLPIYAPAREAAMLGKRRAEAE 66

Query: 63  ALGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSG 122
           A+GV P LIED+LRR+MRESY SE D GFK + P L  +VI+GG GQ+GRLF +M  LSG
Sbjct: 67  AMGVSPQLIEDILRRLMRESYMSEKDVGFKQVNPELGHIVIIGGQGQLGRLFAQMFALSG 126

Query: 123 YQVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGP 181
           Y+VR+L++ DWD A ++   AG+V+V+VPI  T  +I  +L  LP+ CIL DL SVK  P
Sbjct: 127 YEVRLLDKDDWDHADELFDGAGLVLVTVPIATTCSLIRERLDHLPEHCILADLTSVKGAP 186

Query: 182 LQAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRIS 241
           L+AML  H GPV+GLHPMFGPD GSLAKQVVV C GR PE YQW +EQI +WGARL    
Sbjct: 187 LKAMLETHKGPVVGLHPMFGPDVGSLAKQVVVVCHGRAPEKYQWLMEQIGIWGARLVEAD 246

Query: 242 AVEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQ 301
           A  HD+ M  +QA+RHF++F YGL+L  E   ++ LL  SSPIYRLELAMVGRLFAQ  +
Sbjct: 247 AGRHDKAMQLVQAMRHFSSFVYGLNLCREQADIDTLLEFSSPIYRLELAMVGRLFAQSGE 306

Query: 302 LYADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSES 361
           LYADII + E +L  I  +   + +A+ELL+ GD+  FI  F +V +WFG+Y+Q+F +ES
Sbjct: 307 LYADIIFAQEESLTAISDFIDNYRDALELLKTGDRAGFIARFNEVSNWFGNYSQQFLTES 366

Query: 362 RVLLRQANDNR 372
           R +L+  ND R
Sbjct: 367 RAMLQSVNDMR 377


Lambda     K      H
   0.322    0.138    0.404 

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: 403
Number of extensions: 17
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: 373
Length of database: 379
Length adjustment: 30
Effective length of query: 343
Effective length of database: 349
Effective search space:   119707
Effective search space used:   119707
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 (21.9 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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