GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Pseudomonas fluorescens FW300-N2E3

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate AO353_05445 AO353_05445 ornithine decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05445 AO353_05445 ornithine
           decarboxylase
          Length = 387

 Score =  113 bits (282), Expect = 1e-29
 Identities = 111/373 (29%), Positives = 176/373 (47%), Gaps = 27/373 (7%)

Query: 12  KTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGE 71
           +TPF + D   I QA+ + +  F+  K  + YA+KAN  + I+ LL    S  D  SI E
Sbjct: 25  ETPFVVIDTAMIAQAYDDLRAGFEFAK--VYYAVKANPAVEIIDLLKEKGSSFDIASIYE 82

Query: 72  IQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKAR 131
           + + L  G+ P RI +    K + +I    +  +     +S  +L+ I   A    +  R
Sbjct: 83  LDKVLGRGVTPDRISYGNTIKKSKDIRYFYEKGVRLYATDSEADLRNIAKAAPGSKVYVR 142

Query: 132 ISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLL 191
           I    +   D              KFG     A+++ + A+    L P  + FH+GSQ  
Sbjct: 143 ILTEGSTTADWPL---------SRKFGCQTDMAMDLLILARDLG-LVPYGISFHVGSQQR 192

Query: 192 DLEPIIEASQKVAKIAKSLIAL-GIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQ 250
           D+     A  KV  I + L    GI+L+  ++GGG   +Y    T  L  YA+ I+  L+
Sbjct: 193 DISVWDAAIAKVKVIFERLKEEDGINLKLINMGGGFPANYITR-TNSLETYAEEIIRFLK 251

Query: 251 ---GLDLT-IICEPGRSIVAESGELITQ-VLYEKKAQN--KRFVIVDAGMNDFLRPSLYH 303
              G DL  II EPGRS++A +G L+++ VL  +K++   +R+V  D G    L  ++  
Sbjct: 252 EDFGDDLPEIILEPGRSLIANAGILVSEVVLVARKSRTAVERWVYTDVGKFSGLIETMDE 311

Query: 304 AKHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAH--LP-ELEPGDKIAIEKVGAYGS 360
           A     + T  KG E+    + GP C+S+D   ++    LP  L  GD++     GAY +
Sbjct: 312 A-IKFPIWTEKKG-EMEEVVIAGPTCDSADIMYENYKYGLPLNLAIGDRLYWLSTGAYTT 369

Query: 361 S-MASQYNSRPKL 372
           S  A ++N  P L
Sbjct: 370 SYSAVEFNGFPPL 382


Lambda     K      H
   0.319    0.138    0.389 

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: 318
Number of extensions: 14
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: 405
Length of database: 387
Length adjustment: 31
Effective length of query: 374
Effective length of database: 356
Effective search space:   133144
Effective search space used:   133144
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 (21.7 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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