GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Shewanella oneidensis MR-1

Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 200537 SO1362 chorismate mutase/prephenate dehydrogenase (NCBI ptt file)

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



>FitnessBrowser__MR1:200537
          Length = 379

 Score =  426 bits (1096), Expect = e-124
 Identities = 213/369 (57%), Positives = 273/369 (73%), Gaps = 1/369 (0%)

Query: 3   AELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAE 62
           +EL  LR  ID VD+ LL+LL KRL+LVA+VG VK   GLPIY P+REA+MLA RR EA+
Sbjct: 7   SELEHLRGLIDGVDQQLLHLLRKRLDLVAQVGTVKHAAGLPIYAPQREAAMLAKRREEAQ 66

Query: 63  ALGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSG 122
            +G+ P LIED+LRR+MRESY +E D GFK +   L  VVIVGG GQ+G LF++ML LSG
Sbjct: 67  TMGIAPQLIEDILRRLMRESYLNEKDVGFKQVKNDLGSVVIVGGKGQLGGLFQQMLRLSG 126

Query: 123 YQVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGP 181
           YQV++L++ DW +A  + ADAG+V+V+VPI +T  +I  KL  LP+DCIL DL S+K  P
Sbjct: 127 YQVKVLDKDDWQQAECLFADAGLVLVTVPIAITCDIIREKLTQLPRDCILADLTSIKTEP 186

Query: 182 LQAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRIS 241
           +QAML AH GPV+G HPMFGPD GSLAKQVVV C GR+ + YQW LEQI +WGAR+    
Sbjct: 187 MQAMLAAHKGPVVGFHPMFGPDVGSLAKQVVVVCHGREADKYQWLLEQIAIWGARIVEAE 246

Query: 242 AVEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQ 301
              HD  M  +QA+RHF+TF YGL+L +E   +E LL  SSPIYRLELAMVGRLFAQ P+
Sbjct: 247 PECHDNAMQLVQAMRHFSTFVYGLNLCKEEADIETLLKFSSPIYRLELAMVGRLFAQSPE 306

Query: 302 LYADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSES 361
           LYADII + + +   I  Y   + EA+ELL++GD++ FI+ F+ V  WFGD+A +FQ ES
Sbjct: 307 LYADIIFAQQESQHAIGDYLDNYREALELLKRGDREEFINQFQMVAKWFGDFAPQFQRES 366

Query: 362 RVLLRQAND 370
           R++L+  +D
Sbjct: 367 RMMLQSVSD 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: 393
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.

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