GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Shewanella sp. ANA-3

Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 7025863 Shewana3_3012 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)

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



>FitnessBrowser__ANA3:7025863
          Length = 379

 Score =  423 bits (1088), Expect = e-123
 Identities = 212/368 (57%), Positives = 270/368 (73%), Gaps = 1/368 (0%)

Query: 4   ELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAEA 63
           EL  LR  ID VD+ LL+LL KRL+LVA+VG VK   GLPIY P+REA+MLA RR EA+ 
Sbjct: 8   ELEHLRGLIDGVDQQLLHLLRKRLDLVAQVGTVKHAAGLPIYAPQREAAMLAKRREEAKT 67

Query: 64  LGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSGY 123
           +G+ P LIED+LRR+MRESY +E D GFK +   L  VVIVGG GQ+G LF++ML+LSGY
Sbjct: 68  MGIAPQLIEDILRRLMRESYLNEKDVGFKQVKNDLGSVVIVGGKGQLGGLFQQMLSLSGY 127

Query: 124 QVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGPL 182
           QV++L++ DW +A  + ADAG+V+V+VPI +T  +I  KL  LP++CIL DL S+K  P+
Sbjct: 128 QVKVLDKDDWQQAETLFADAGLVLVTVPIAITCDIIREKLTQLPQECILADLTSIKTEPM 187

Query: 183 QAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRISA 242
            AML AH GPV+G HPMFGPD GSLAKQVVV C GR  + YQW LEQI +WGAR+     
Sbjct: 188 NAMLAAHKGPVVGFHPMFGPDVGSLAKQVVVVCHGRGADKYQWLLEQIGIWGARIVEAEP 247

Query: 243 VEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQL 302
             HD  M  +QA+RHF+TF YGL+L +E   +E LL  SSPIYRLELAMVGRLFAQ P+L
Sbjct: 248 ERHDNAMQLVQAMRHFSTFVYGLNLCKEEADIETLLQFSSPIYRLELAMVGRLFAQSPEL 307

Query: 303 YADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSESR 362
           YADII + + +   I  Y   + EA+ELL++GD+ AFI  F+ V  WFGD+A +FQ ESR
Sbjct: 308 YADIIFAQQDSQHAIGDYLDNYREALELLKRGDRDAFISQFQTVAKWFGDFAPQFQRESR 367

Query: 363 VLLRQAND 370
           ++L+  +D
Sbjct: 368 MMLQSVSD 375


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: 390
Number of extensions: 14
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 (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