GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Pseudomonas fluorescens GW456-L13

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate PfGW456L13_3943 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3943
          Length = 336

 Score =  273 bits (697), Expect = 6e-78
 Identities = 142/335 (42%), Positives = 217/335 (64%), Gaps = 1/335 (0%)

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

Query: 61  EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120
           +FD+S+V +A F+AG  +S  +A  A +AG  VID +     +   P VVPE N + +A 
Sbjct: 61  QFDFSKVQLAFFAAGPAVSLSFASRATDAGCSVIDLSGALPAE-KAPQVVPEANAQVLAG 119

Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180
            +    +++P+ S   + V L P+ D + ++RI++T   +VS  G+  + ELA QTA+LL
Sbjct: 120 LKKPFQVSSPSPSATTLAVVLAPLMDLLDLQRISLTASLAVSAQGREAVSELARQTAELL 179

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

Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVRDAGGKDHVLVGRVRN 300
           VF+G + +V +++ + ID  +V   LE   GIEL    D+PT V DA G+D V VGRVR+
Sbjct: 240 VFFGDSYSVTLQSASEIDLGKVNAALEDAPGIELVEAGDYPTPVGDAVGQDVVYVGRVRH 299

Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVRD 335
            I   S +NLW+ +DNVRKGAA NAVQ+AELL++D
Sbjct: 300 GIDDTSELNLWLTSDNVRKGAALNAVQLAELLIKD 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: 258
Number of extensions: 13
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