GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Shewanella loihica PV-4

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 5208561 Shew_1072 chorismate mutase (RefSeq)

Query= BRENDA::O30012
         (620 letters)



>FitnessBrowser__PV4:5208561
          Length = 654

 Score =  150 bits (378), Expect = 2e-40
 Identities = 108/376 (28%), Positives = 195/376 (51%), Gaps = 28/376 (7%)

Query: 262 KAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSK 321
           K   +   R  I ++D+ +L L+ +R   +  +AR K     PI     E+E L  ++ +
Sbjct: 3   KPHPLSHTREQITALDNELLALLAKRRALSLDVARSKEVDIRPIRDTQREKELLARLVKQ 62

Query: 322 TT---LNPVKLKEIFEGIM--SLAKEEEY-------KVAGVKYTIAVLGPQGSFSEEMAL 369
                L+   +  +++ I+  S+  ++ Y        +   +Y IA LG +GS+S   A 
Sbjct: 63  GREQGLDAHYVLSLYQSIIEDSVLNQQAYLQGRANPDLQKQQYNIAYLGARGSYSYLAAT 122

Query: 370 KLVGSR---VPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVF 426
           +    R   +    C + DEI++ VESG  DYG +PIEN+ +G++  V D L +  + + 
Sbjct: 123 RYCERRQVGMQDLGCKSFDEIVQAVESGHADYGFLPIENTSSGSINEVYDVLQHTSLAIV 182

Query: 427 GEAKLEVNHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARM 486
           GE  +EV HCL+AK    +K+IKTIY+HPQ ++QC  +++ +     + Y +S+++A   
Sbjct: 183 GETTIEVGHCLLAKPGTNVKQIKTIYAHPQPISQCSRYLSQH-GEFKLEYCSSSAEAMER 241

Query: 487 L----DDYSAAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGKI---TS 539
           +    D+  AAI S      Y+L  +   + + K  N +RF ++ R++     ++   T+
Sbjct: 242 VLEADDNSVAAIGSVEGGALYQLEAVEHELANQK-INQSRFIVVARKAIAVPEQLPAKTT 300

Query: 540 LFFGVEDKPGALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----L 595
           L      KPGAL + L +      N+ KLESRP      + +F+++++A L  ++    L
Sbjct: 301 LIMATGQKPGALVEALLILKAHDLNMSKLESRPIPGTPWEEMFYLDLDANLASDEMQQAL 360

Query: 596 LDLKQVTTFYKVVGVF 611
            +L+++T F KV+G +
Sbjct: 361 KELERITRFIKVLGCY 376


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: 745
Number of extensions: 34
Number of successful extensions: 4
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: 654
Length adjustment: 38
Effective length of query: 582
Effective length of database: 616
Effective search space:   358512
Effective search space used:   358512
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: 54 (25.4 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