GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Streptacidiphilus oryzae TH49

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_037574263.1 BS73_RS19430 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000744815.1:WP_037574263.1
          Length = 425

 Score =  286 bits (733), Expect = 6e-82
 Identities = 160/410 (39%), Positives = 237/410 (57%), Gaps = 18/410 (4%)

Query: 21  QIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQV 80
           Q  P+ A+R E   +++  GR +LDF  GI V +TGH HPKVVAA + Q+ +L H  +  
Sbjct: 10  QATPVLAERGEGVYLYEESGRRHLDFTAGIGVTSTGHCHPKVVAAAQEQVGRLVHGQYTT 69

Query: 81  LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHG 140
           + ++P L L E + + +P         V +GSEAVE A+++A+ AT R   + F G++HG
Sbjct: 70  VMHKPLLTLSERLGEVLPAGL-DSLFFVNSGSEAVEAAMRLAKQATARPNIVVFQGSFHG 128

Query: 141 RTHYTLALTGKVNPYSAGMG-LMPGHVYRALYPCPLH----GISEDDA----IASIHRIF 191
           RT    ++T     + +G G LMPG V  A +P   H    G+ E+ A    +  +  + 
Sbjct: 129 RTLAAASMTTSATKFRSGYGPLMPG-VAIAPFPHAAHYARYGMDEEAATRFALRELDELL 187

Query: 192 KNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTL 251
              +AP D AA ++EPV GEGG+  ++ AF++ LR   D HGI+LI DEVQ+G GRTG  
Sbjct: 188 ATVSAPADTAAFIVEPVLGEGGYVPANSAFLRGLRERADRHGILLILDEVQTGFGRTGRF 247

Query: 252 FAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEV 311
           +  +     PD+   AK +A GFPL+ +     +M+   PG  GGTY GN +AC AA+  
Sbjct: 248 WGHDHFDGRPDILVTAKGLASGFPLSAIAAPRALMEKAWPGSQGGTYGGNAVACAAAIAT 307

Query: 312 LKVFEQENLLQKANDLGQKLKDGLLAIAEKHPE-----IGDVRGLGAMIAIELFEDGDHN 366
           L V ++E L++ A + G++L  GL  +A  HP      IGDVRGLG M   E F   D  
Sbjct: 308 LDVIQEEKLVENAAERGEQLFAGLREVAAAHPAGGRGGIGDVRGLGLMAGTE-FTTAD-G 365

Query: 367 KPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEI 416
           +PD    A++ A A ++GL+LL+CGP   V+R++ PL ++  QI +GL +
Sbjct: 366 EPDGATAAKVHAAAAERGLLLLTCGPRGEVVRMIPPLVVDAEQIDEGLRL 415


Lambda     K      H
   0.320    0.137    0.401 

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: 485
Number of extensions: 21
Number of successful extensions: 5
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: 426
Length of database: 425
Length adjustment: 32
Effective length of query: 394
Effective length of database: 393
Effective search space:   154842
Effective search space used:   154842
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: 51 (24.3 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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