GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Paraburkholderia bryophila 376MFSha3.1

Align aspartate 4-decarboxylase (EC 4.1.1.12) (characterized)
to candidate H281DRAFT_04749 H281DRAFT_04749 aspartate 4-decarboxylase

Query= BRENDA::Q53IZ1
         (531 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04749 H281DRAFT_04749
           aspartate 4-decarboxylase
          Length = 554

 Score =  616 bits (1589), Expect = 0.0
 Identities = 315/526 (59%), Positives = 388/526 (73%), Gaps = 7/526 (1%)

Query: 8   LANLSPFELKDELIKVASG-----KANRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAES 62
           LA LSPFELKDELIK A G      AN  MLNAGRGNPNFLAT PR  F++LGLFA  ES
Sbjct: 18  LAALSPFELKDELIKAAGGGAVERPANASMLNAGRGNPNFLATIPRHGFWQLGLFAMRES 77

Query: 63  ELSYSYMTVGVGGLAKLDGIEGRFERFIAEHRDQEGVKFLGKSLSYVRDQLGLDPAAFLH 122
           E S++YM  GVGG  + +G+E RF+ F+ E++   G+ FL  ++SYVRDQLGL    FL+
Sbjct: 78  ERSFAYMPEGVGGFPRREGLEERFDLFLRENKGVAGIDFLRGAVSYVRDQLGLSAGDFLY 137

Query: 123 EMVDGILGCNYPVPPRMLTVSEQIVRQYIVREMAGGAVPPESVDLFAVEGGTAAMAYIFE 182
           EM +GILG NYPVP RML +SE IV QY+ REM G        D+FAVEGGTAAM YIF 
Sbjct: 138 EMCEGILGSNYPVPDRMLKLSEVIVGQYLRREMIGRHPFVGEFDVFAVEGGTAAMTYIFN 197

Query: 183 SLRISGLLKAGDKVAIGMPVFTPYIEIPELAQYDLKEVPIHADPDNGWQYSDAELDKLKD 242
           ++R + L+K GD +A+GMP+FTPYIEIP L  Y L  V ++A  +NGWQY+  ELDKL+D
Sbjct: 198 TMRENHLIKPGDTIALGMPIFTPYIEIPRLNDYQLNVVNLNAGVENGWQYTKEELDKLRD 257

Query: 243 PDVKIFFCVNPSNPPSVKMDQRSLDRVRAIVAEQRPDLLILTDDVYGTFADEFQSLFSVC 302
           P VK FF VNPSNPPSVKMD  SL  +  IV E RPDL++LTDDVYGTFAD+F SLF++ 
Sbjct: 258 PKVKAFFLVNPSNPPSVKMDDESLQYIADIVKE-RPDLILLTDDVYGTFADDFVSLFALA 316

Query: 303 PRNTLLVYSFSKYFGATGWRLGVIAAHKDNVFDHALSQLPESAKKALDHRYRSLLPDVRS 362
           P+NT+LVYS+SKYFGATGWRLG IA H+DNV D  +S+LP+  KK L  RY S+  +   
Sbjct: 317 PKNTILVYSYSKYFGATGWRLGTIATHRDNVLDRLISELPKDVKKQLHERYESITTEPEK 376

Query: 363 LKFIDRLVADSRVVALNHTAGLSTPQQVQMVLFSLFALMDEADAYKQALKQLIRRREATL 422
           LKFIDRLVADSR VALNHTAGLSTPQQVQMVLFSLF+LMD  DAYK ALK+LIR+R+  L
Sbjct: 377 LKFIDRLVADSRTVALNHTAGLSTPQQVQMVLFSLFSLMDTPDAYKNALKRLIRKRKQAL 436

Query: 423 YRELGMP-PLENPNSVNYYTLIDLQNVTCRLYGEAFSQWAVQQSSTGDMLFRVADETGIV 481
           Y E+G+     +PN V+YYT++D + +  R++G  F  W ++ +   ++LFR+A E  +V
Sbjct: 437 YEEVGIAFDDSDPNQVDYYTILDAEYLGERMFGREFVDWQLKSTQPTELLFRLAREARVV 496

Query: 482 LLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRRLADELYEQYKA 527
           LLPG GFG+   SGR SLANLNE +Y  IGRA+RRL +E  E++ A
Sbjct: 497 LLPGLGFGTQHASGRVSLANLNESDYRQIGRAVRRLIEEYVERFNA 542


Lambda     K      H
   0.321    0.138    0.400 

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: 809
Number of extensions: 33
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: 531
Length of database: 554
Length adjustment: 35
Effective length of query: 496
Effective length of database: 519
Effective search space:   257424
Effective search space used:   257424
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: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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