GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Sphingomonas koreensis DSMZ 15582

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Ga0059261_1288 Ga0059261_1288 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q8YTF2
         (403 letters)



>FitnessBrowser__Korea:Ga0059261_1288
          Length = 401

 Score =  332 bits (852), Expect = 9e-96
 Identities = 163/381 (42%), Positives = 235/381 (61%), Gaps = 3/381 (0%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           RI++LPPYV A ++ ++A AR  G D+IDLGMGNPD   PQ V+D   +  Q P  HGY 
Sbjct: 7   RIKRLPPYVIAEVNGMRAAARAAGEDIIDLGMGNPDLPPPQHVIDKLCEVAQKPSAHGYS 66

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
             +G    RRA  N+Y RR+GV +DP+SE +  +GSKEGL+ LA A   PGDV+L P+P+
Sbjct: 67  QSKGIPGLRRAQANYYGRRFGVDVDPESEVVVTMGSKEGLASLATAITAPGDVILAPNPS 126

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190
           YP H  G +IAG T+ ++   P+  +   L         +  IL  NYPSNPT  T    
Sbjct: 127 YPIHTFGFIIAGATIRAVPTTPDEHYFESLERAMNFTVPRPSILVVNYPSNPTAETVDLA 186

Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250
           F+E +VA+A++ ++ ++ DL Y+EL +DG    S+L++ GAKD+ +EF +LSKTY+MAGW
Sbjct: 187 FYERLVAWAKENKVWIISDLAYSELYYDGKPTVSILQVKGAKDVAIEFTSLSKTYSMAGW 246

Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310
           R+GF VGN+ +I  +  +K+ LDYG F  +Q AA  AL  P   +   +Q Y  RRD L+
Sbjct: 247 RIGFAVGNKQLIAAMTRVKSYLDYGAFTPVQAAACAALNGPQDIVEANRQLYHKRRDVLV 306

Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367
           +  G  GWD+P   A+M+ W   P     +GS +F+  LL    V V PG  +G  GEG+
Sbjct: 307 ESFGRAGWDIPAPPASMFAWAPLPPALAHLGSLEFSKQLLSHAKVAVAPGVGYGENGEGF 366

Query: 368 VRISLIADCDRLGEALDRIKQ 388
           VRI+++ +  RL +A   +++
Sbjct: 367 VRIAMVENEQRLRQAARNVRK 387


Lambda     K      H
   0.321    0.140    0.427 

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: 457
Number of extensions: 24
Number of successful extensions: 2
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: 403
Length of database: 401
Length adjustment: 31
Effective length of query: 372
Effective length of database: 370
Effective search space:   137640
Effective search space used:   137640
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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