GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Pseudomonas fluorescens FW300-N2E3

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate AO353_20645 AO353_20645 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20645
          Length = 336

 Score =  266 bits (679), Expect = 7e-76
 Identities = 137/335 (40%), Positives = 211/335 (62%), Gaps = 1/335 (0%)

Query: 1   MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60
           MSQ F++A+ GATG VGET++++L+ER+FPV  L LLAS  S G +  F GK VRV+ V+
Sbjct: 1   MSQSFDIAVVGATGTVGETLVQILEERDFPVANLHLLASSESAGHSVPFRGKNVRVREVD 60

Query: 61  EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120
           EFD+S+V +  F+AG  ++  +AP A  AG  +ID +     +   P VVPE N + +A 
Sbjct: 61  EFDFSKVQLVFFAAGPAVTLSFAPRATAAGCALIDLSGALPAE-QAPQVVPEANSQVLAG 119

Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180
            +    +++P+ S   + V L P+ + + ++R+ VT   +VS  G+  + ELA QTA+LL
Sbjct: 120 LKKPFQVSSPSASATTLAVVLAPLRELLDLQRVTVTASLAVSAQGREAVSELARQTAELL 179

Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240
           N  P E   F +Q+AFN + Q+      G+T  E ++V E +++   P + ++ TC++ P
Sbjct: 180 NVRPLEPRFFDRQMAFNLLAQVGTPDAQGHTLLEKRLVRELREVMAQPLLKISVTCIQAP 239

Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVRDAGGKDHVLVGRVRN 300
           VF+G + +V +++   +D   V   LE   G+EL    D+PT V DA G+D V VGRVR+
Sbjct: 240 VFFGDSFSVTLQSAKAVDLAAVNAALEAAPGVELVEAGDYPTPVGDAVGQDVVYVGRVRS 299

Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVRD 335
            I   + +N+W+ +DNVRKGAA NAVQ+AELL++D
Sbjct: 300 GIDDPAELNVWLTSDNVRKGAALNAVQVAELLIKD 334


Lambda     K      H
   0.319    0.135    0.395 

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: 252
Number of extensions: 10
Number of successful extensions: 2
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: 337
Length of database: 336
Length adjustment: 28
Effective length of query: 309
Effective length of database: 308
Effective search space:    95172
Effective search space used:    95172
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: 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