GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azospirillum brasilense Sp245

Align aspartate 4-decarboxylase (EC 4.1.1.12) (characterized)
to candidate AZOBR_RS30390 AZOBR_RS30390 aspartate aminotransferase

Query= BRENDA::Q53IZ1
         (531 letters)



>FitnessBrowser__azobra:AZOBR_RS30390
          Length = 543

 Score =  783 bits (2023), Expect = 0.0
 Identities = 381/524 (72%), Positives = 444/524 (84%)

Query: 2   SKDYRSLANLSPFELKDELIKVASGKANRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAE 61
           S DY   A LSPFELKDELIK+ASG+ NRLMLNAGRGNPNFLAT PRRAFFRLGLFA AE
Sbjct: 3   SIDYSRYAKLSPFELKDELIKLASGRENRLMLNAGRGNPNFLATLPRRAFFRLGLFAVAE 62

Query: 62  SELSYSYMTVGVGGLAKLDGIEGRFERFIAEHRDQEGVKFLGKSLSYVRDQLGLDPAAFL 121
           +ELS+SYM  GVGGL +L+GIEGRFER+++EHRDQEGV FLG++LSYVRDQLGL  + FL
Sbjct: 63  AELSFSYMPNGVGGLPRLEGIEGRFERYVSEHRDQEGVVFLGRALSYVRDQLGLSGSGFL 122

Query: 122 HEMVDGILGCNYPVPPRMLTVSEQIVRQYIVREMAGGAVPPESVDLFAVEGGTAAMAYIF 181
           HEMV+G+LG NYPVPPRML +SE +VR Y+V+EM GG +PP SVDLFAVEGGTAAM YIF
Sbjct: 123 HEMVEGVLGANYPVPPRMLAISEDVVRHYLVKEMVGGFLPPGSVDLFAVEGGTAAMTYIF 182

Query: 182 ESLRISGLLKAGDKVAIGMPVFTPYIEIPELAQYDLKEVPIHADPDNGWQYSDAELDKLK 241
            S++ +GL++ GDKVAIG+PVFTPYIEIPEL +Y L EV I+ADP  GWQY DAELDKLK
Sbjct: 183 NSMKQNGLVERGDKVAIGLPVFTPYIEIPELDEYGLTEVAINADPAKGWQYPDAELDKLK 242

Query: 242 DPDVKIFFCVNPSNPPSVKMDQRSLDRVRAIVAEQRPDLLILTDDVYGTFADEFQSLFSV 301
           DP VK+FFCVNPSNPPSVKMD RSLDR+ AIV  +R DL+ILTDDVYGTFAD F+SLF+V
Sbjct: 243 DPAVKVFFCVNPSNPPSVKMDDRSLDRIAAIVKNERKDLIILTDDVYGTFADNFRSLFAV 302

Query: 302 CPRNTLLVYSFSKYFGATGWRLGVIAAHKDNVFDHALSQLPESAKKALDHRYRSLLPDVR 361
           CP NT+LVYSFSKYFGATGWRLGVIA HK NV D  ++ LPE  K ALD RY SL+PDVR
Sbjct: 303 CPENTMLVYSFSKYFGATGWRLGVIATHKTNVCDQRIAALPEERKAALDRRYGSLVPDVR 362

Query: 362 SLKFIDRLVADSRVVALNHTAGLSTPQQVQMVLFSLFALMDEADAYKQALKQLIRRREAT 421
            L+FIDRLVADSR VALNHTAGLSTPQQVQMVLFSLFALMDE D YK  LK++IRRREA 
Sbjct: 363 GLRFIDRLVADSRTVALNHTAGLSTPQQVQMVLFSLFALMDEQDGYKAELKKVIRRREAA 422

Query: 422 LYRELGMPPLENPNSVNYYTLIDLQNVTCRLYGEAFSQWAVQQSSTGDMLFRVADETGIV 481
           LYRELG+P L +PN+V+YYTL+DL+++  +LYG  ++ W        D+LFR+A ETGIV
Sbjct: 423 LYRELGLPTLSDPNAVDYYTLLDLEDIALKLYGPDYAAWVKANFVPNDLLFRIAAETGIV 482

Query: 482 LLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRRLADELYEQY 525
           LLPG+GFG+ +P+ R SLANLNEYEYAAIGR+LR +AD+ +E++
Sbjct: 483 LLPGKGFGTLQPAARVSLANLNEYEYAAIGRSLRGMADQSHEEF 526


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: 909
Number of extensions: 27
Number of successful extensions: 1
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: 543
Length adjustment: 35
Effective length of query: 496
Effective length of database: 508
Effective search space:   251968
Effective search space used:   251968
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