GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Pseudomonas putida KT2440

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate PP_1992 PP_1992 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Putida:PP_1992
          Length = 334

 Score =  250 bits (638), Expect = 4e-71
 Identities = 134/334 (40%), Positives = 201/334 (60%), Gaps = 3/334 (0%)

Query: 1   MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60
           M+   ++A+ GATG+VGE ++++L+E  FPV  L LLAS  S G +  F GK ++V+ V+
Sbjct: 1   MTHPLDIAVVGATGSVGEALVQILEELAFPVATLHLLASMESAGSSVMFAGKKLKVREVD 60

Query: 61  EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120
            FD++QV +A F+ G  +S  +A  A +AG  VID +       D   +VPE N E +A 
Sbjct: 61  SFDFAQVKLAFFATGAAVSRSFAGKALQAGCTVIDLSGGLD---DALALVPEANAERLAS 117

Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180
                 I +P  + + + VAL P+   + IER+ V    +VS  G+  + ELA QTA+LL
Sbjct: 118 LSLPARIVSPCSAAVALAVALAPLKGLLDIERVQVMAALAVSAQGREAVSELARQTAELL 177

Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240
           N  P E   F +Q+AFN + Q+    + G+T  E ++V E + +   P + ++ +CV+VP
Sbjct: 178 NARPLEPRFFDRQVAFNLLAQVGAADEQGHTALERRLVSELRVLLGLPELKISVSCVQVP 237

Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVRDAGGKDHVLVGRVRN 300
           VF+G + +V V++R P+D   V   LE  D IE     D+PT V DA G+D V VGRVR+
Sbjct: 238 VFFGDSFSVAVQSRRPVDLAAVNQALEAADSIERVENDDYPTPVGDAVGQDVVYVGRVRH 297

Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVR 334
            +     +NLW+  DNVRKGAA NAVQ+A+LL++
Sbjct: 298 GVDEDQQLNLWLTTDNVRKGAALNAVQVAQLLIK 331


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: 239
Number of extensions: 9
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: 334
Length adjustment: 28
Effective length of query: 309
Effective length of database: 306
Effective search space:    94554
Effective search space used:    94554
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