GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella amazonensis SB2B

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 6936711 Sama_0898 prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= BRENDA::Q9YEJ7
         (270 letters)



>FitnessBrowser__SB2B:6936711
          Length = 659

 Score =  101 bits (252), Expect = 4e-26
 Identities = 76/223 (34%), Positives = 112/223 (50%), Gaps = 10/223 (4%)

Query: 17  RETVVEVEG--VRIGGGSKAVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKPRTSP 74
           +ETV EV+   + IG G    +A     ++ E        +K AG   L       R  P
Sbjct: 425 KETVSEVQAGALLIGNGHSGALAMLSLPDTLEGFEPFLKQLKAAGFAGLVLDNLSERPDP 484

Query: 75  YSFQGLGLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLRE 134
                   + L    +A ++ GL     V     +E      +++ I  + M N PLL  
Sbjct: 485 -------AKALDACTKAAEKFGLITAAAVNREDELEHAISRVELILIRGKQMFNQPLLER 537

Query: 135 VGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVA 194
           +G+   PV+L+R     ++ELLAAA+ IL EGN Q++L E G+ +F+ ST  TLD+A + 
Sbjct: 538 LGKLHLPVVLERNTMADIDELLAAADTILAEGNQQLMLCESGVSSFKSSTLATLDLAGLV 597

Query: 195 VLKEATHLPVIVDPSHPAGRRSLVPALAKAGLAAGADGLIVEV 237
            LK  +HLPV+V+PS+ A      P  AKA    GADGL++EV
Sbjct: 598 ELKARSHLPVLVNPSY-AVTPEACPRQAKAVKRLGADGLLLEV 639


Lambda     K      H
   0.318    0.136    0.392 

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: 269
Number of extensions: 6
Number of successful extensions: 1
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: 270
Length of database: 659
Length adjustment: 32
Effective length of query: 238
Effective length of database: 627
Effective search space:   149226
Effective search space used:   149226
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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