GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Pseudomonas fluorescens FW300-N2C3

Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate AO356_27140 AO356_27140 homoserine dehydrogenase

Query= curated2:Q58997
         (336 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27140
          Length = 349

 Score =  210 bits (535), Expect = 4e-59
 Identities = 134/338 (39%), Positives = 190/338 (56%), Gaps = 9/338 (2%)

Query: 3   IIIVGFGAIGKGIAKVLYDKKD-YLKKNYEEFKVVAITDSS-GAAIDEDGLDLLKAIEVK 60
           I ++GFG + + + +++ DK   +  +     K+V ++D   G+ I++DGLD  +   V 
Sbjct: 6   IALLGFGGVNRALTQLIADKNSRWADELGFTLKIVGVSDLYLGSIINKDGLDAHELAAVP 65

Query: 61  EKTGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVVT 120
              G  +  P    E ++  VI+   AD+V E T +N   G+PA T    + +    VVT
Sbjct: 66  AAKGGFRTLPGGSAEPANETVIRFSGADIVAEATFTNPVDGEPATTFCRWALEKGVSVVT 125

Query: 121 ANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGTT 180
            NKGP+AL  + L   A   G  F  E SV    P+I LAKE+LAG+EI   +GILNGT+
Sbjct: 126 TNKGPVALHAQSLKTLADSAGARFEFEGSVMSGTPVIRLAKESLAGSEITGFKGILNGTS 185

Query: 181 NYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIKD 240
           N++L+ ME  GLDF +A+ +A+ELG AE DPT D+EG D   K+VILAN ++G      D
Sbjct: 186 NFVLSSME-TGLDFSSAVAKAQELGYAEADPTADVEGHDVRLKVVILANELLGAKLKPSD 244

Query: 241 VKVKGISRITPEALFLANKRGYTIKLIGQIK---DGYL--IVEPMLVPIDSPLN-VKGTL 294
           V  KGIS IT + +  A K     KLIG  +   DG +   V P L+P    L+ V G  
Sbjct: 245 VLCKGISEITAKDIAEATKVNARWKLIGSAEKRSDGSISASVSPQLLPSSDALSAVSGAT 304

Query: 295 NVAMFETDLAKEVVVVGRGAGPIETASAILSDLIHIYN 332
           N   F T +   V VVG GAG  ETA A+L+D++ I+N
Sbjct: 305 NAITFSTAILGPVTVVGAGAGRFETAFALLADIVSIHN 342


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: 295
Number of extensions: 11
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: 336
Length of database: 349
Length adjustment: 29
Effective length of query: 307
Effective length of database: 320
Effective search space:    98240
Effective search space used:    98240
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