GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Burkholderia phytofirmans PsJN

Align aspartate 4-decarboxylase (EC 4.1.1.12) (characterized)
to candidate BPHYT_RS03850 BPHYT_RS03850 aspartate aminotransferase

Query= BRENDA::Q53IZ1
         (531 letters)



>FitnessBrowser__BFirm:BPHYT_RS03850
          Length = 554

 Score =  617 bits (1592), Expect = 0.0
 Identities = 314/526 (59%), Positives = 391/526 (74%), Gaps = 7/526 (1%)

Query: 8   LANLSPFELKDELIKVASGKA-----NRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAES 62
           +A LSPFELKDELIK A G A     N  MLNAGRGNPNFLAT PR  F++LGLFA  ES
Sbjct: 18  MAALSPFELKDELIKAAGGAAVERPANASMLNAGRGNPNFLATIPRHGFWQLGLFAMRES 77

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

Query: 123 EMVDGILGCNYPVPPRMLTVSEQIVRQYIVREMAGGAVPPESVDLFAVEGGTAAMAYIFE 182
           EM +GIL  NYPVP RML +SE IV QY+ +EM G        D+FAVEGGTAAM YIF 
Sbjct: 138 EMCEGILASNYPVPDRMLKLSELIVGQYLRKEMIGDHPFVGEFDVFAVEGGTAAMTYIFN 197

Query: 183 SLRISGLLKAGDKVAIGMPVFTPYIEIPELAQYDLKEVPIHADPDNGWQYSDAELDKLKD 242
           ++R + L+KAGD +A+GMP+FTPYIEIP L  Y L  V + AD  NGWQYS  ELDKL+D
Sbjct: 198 TMRENHLIKAGDTIALGMPIFTPYIEIPRLNDYRLNVVNLEADVANGWQYSKKELDKLRD 257

Query: 243 PDVKIFFCVNPSNPPSVKMDQRSLDRVRAIVAEQRPDLLILTDDVYGTFADEFQSLFSVC 302
           P VK FF VNPSNPPSVKMD  SL R  A + ++RPDL++LTDDVYGTFAD+F SLF++ 
Sbjct: 258 PKVKAFFLVNPSNPPSVKMDDESL-RYIADIVKERPDLILLTDDVYGTFADDFVSLFALA 316

Query: 303 PRNTLLVYSFSKYFGATGWRLGVIAAHKDNVFDHALSQLPESAKKALDHRYRSLLPDVRS 362
           P+NT+LVYS+SKYFGATGWRLG IA H+DNV D  ++ LP+ AKK L  RY S+  +   
Sbjct: 317 PKNTILVYSYSKYFGATGWRLGTIATHRDNVLDKLIADLPKDAKKQLHERYESITTEPDK 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 YEEVGISFKDDDPNQVDYYTILDVEFLGERMFGREFVDWLLKNTEPSELLFRLAREARVV 496

Query: 482 LLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRRLADELYEQYKA 527
           LLPG GFG+  PSGR SLANLNE +Y  IGRA+R+L +EL E++ A
Sbjct: 497 LLPGLGFGTQHPSGRVSLANLNESDYRQIGRAMRKLIEELVERFNA 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: 811
Number of extensions: 31
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.

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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