GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Pseudomonas putida KT2440

Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate PP_0664 PP_0664 homoserine dehydrogenase

Query= curated2:Q58997
         (336 letters)



>FitnessBrowser__Putida:PP_0664
          Length = 347

 Score =  214 bits (546), Expect = 2e-60
 Identities = 131/339 (38%), Positives = 192/339 (56%), Gaps = 9/339 (2%)

Query: 3   IIIVGFGAIGKGIAKVLYDKKDYLKKNYE-EFKVVAITDSS-GAAIDEDGLDLLKAIEVK 60
           I +VGFG + + +A+++ ++    +       K+V +TD   G+ ID DGLD      + 
Sbjct: 6   IALVGFGGVNRALAQLIAERNARWQHELGFGLKIVGVTDLFLGSVIDRDGLDAAVLAALP 65

Query: 61  EKTGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVVT 120
            + G + + P+   E  +  VIK+  AD++ E T +N + G+PA T    + +  KHVVT
Sbjct: 66  AQKGALAHIPQGSAEAFNEAVIKQSGADIIAEATFTNPKDGEPAATFCRWALEAGKHVVT 125

Query: 121 ANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGTT 180
            NKGP+AL  + L   AK + V F +E +V    P++ +A++TLAG  ++   GILNGT+
Sbjct: 126 TNKGPIALHAQALKALAKANNVSFEYEGAVMSGTPVLRMARQTLAGAGLVGFEGILNGTS 185

Query: 181 NYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIKD 240
           NY+LT+ME EGL F  A+ +A+ LG AE DPT D+EG D   K+VILAN ++G    + D
Sbjct: 186 NYVLTRME-EGLGFNEAVAQAQALGFAEADPTADVEGHDVRLKVVILANELLGACLQVGD 244

Query: 241 VKVKGISRITPEALFLANKRGYTIKLIGQIK-----DGYLIVEPMLVPIDSPL-NVKGTL 294
           V   GIS I   A+  A   G   KLIG  +          VE  L+P   PL  + G  
Sbjct: 245 VACSGISAIDSAAIERARAAGERWKLIGSARREAGGSVRASVEAKLLPGHHPLAGILGAT 304

Query: 295 NVAMFETDLAKEVVVVGRGAGPIETASAILSDLIHIYNS 333
           N   F+T+L   V V G GAG IETA A+LSD++ I+ +
Sbjct: 305 NALAFDTELLGAVTVSGPGAGRIETAFALLSDIVAIHTA 343


Lambda     K      H
   0.314    0.135    0.366 

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: 280
Number of extensions: 15
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: 336
Length of database: 347
Length adjustment: 29
Effective length of query: 307
Effective length of database: 318
Effective search space:    97626
Effective search space used:    97626
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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