GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Escherichia coli BW25113

Align shikimate dehydrogenase (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate 15811 b1692 quinate/shikimate 5-dehydrogenase, NAD(P)-binding (NCBI)

Query= BRENDA::Q6PUG0
         (521 letters)



>FitnessBrowser__Keio:15811
          Length = 288

 Score =  115 bits (287), Expect = 3e-30
 Identities = 97/299 (32%), Positives = 140/299 (46%), Gaps = 32/299 (10%)

Query: 236 MDTDTK--VFGLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVDD--LKEFFRVYSSPD 291
           MD   K  + GL++ P+ HS  P + N      G    Y+   VD+           +  
Sbjct: 1   MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALK 60

Query: 292 FAGFSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDA 351
             G  V +P K+    + DE+ P AK +GA+NTI+    DG L GYNTD    I AI+++
Sbjct: 61  MRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVND--DGYLRGYNTDGTGHIRAIKES 118

Query: 352 LKVNGLTNGAAFLPSPLAGKLFVLVGAGGAGRAL-AFGAKSRRAEIVIF---DIDFDRAK 407
                           + GK  VL+GAGGA  A+ A GA     EI +F   D  FD+A 
Sbjct: 119 -------------GFDIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKAL 165

Query: 408 ALAAAVSGE---ALPFENLASFQPEKGA-----ILANATPIGMHPNKDRIPVSEAS-LKD 458
           A A  V+      +   +LA  Q    A     IL N T +GM P ++   V++ S L  
Sbjct: 166 AFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHP 225

Query: 459 YVVVFDAVYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFTRTKAPEEFMRDIV 517
            ++V + VY P  T LL+ A+ AG  T+ G  M L Q   QF L+T    P E+++ ++
Sbjct: 226 GLLVTECVYNPHMTKLLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVM 284


Lambda     K      H
   0.320    0.138    0.405 

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: 309
Number of extensions: 8
Number of successful extensions: 3
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: 521
Length of database: 288
Length adjustment: 30
Effective length of query: 491
Effective length of database: 258
Effective search space:   126678
Effective search space used:   126678
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: 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