GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_05445
          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:

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