GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Dechlorosoma suillum PS

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Dsui_2909 Dsui_2909 aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q8YTF2
         (403 letters)



>lcl|FitnessBrowser__PS:Dsui_2909 Dsui_2909
           aspartate/tyrosine/aromatic aminotransferase
          Length = 395

 Score =  355 bits (910), Expect = e-102
 Identities = 177/380 (46%), Positives = 246/380 (64%), Gaps = 3/380 (0%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           RI++LPPYVF    ELK  AR +G D+ID+ MGNPDGATP+ +VD  + A Q    HGY 
Sbjct: 6   RIKRLPPYVFNITGELKMAARRRGEDIIDMSMGNPDGATPKHIVDKMVDATQRGDTHGYS 65

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
             +G    R+AI +WY RRY V  DPDSEA+  +GSKEGL+HL +A ++ GD VLVP+P+
Sbjct: 66  VSKGIPRLRKAICDWYLRRYNVEFDPDSEAVVTIGSKEGLAHLMLATLDRGDTVLVPNPS 125

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190
           YP H  G +IAG    S+ +  + D+  +L     E   K K++   +PSNPT      +
Sbjct: 126 YPIHIYGAIIAGANTRSVRMTDDVDFFEELQRAIRECTPKPKMMILGFPSNPTARCVELD 185

Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250
           FFE +VA A++++IL+VHDL YA++ FDGY+  S++E+PGA+D+ VEF T+SK+YNMAGW
Sbjct: 186 FFERVVALAKEHDILVVHDLAYADIVFDGYRAPSIMEVPGARDVAVEFFTMSKSYNMAGW 245

Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310
           RVG++VGN+ +   L  +K+  DYG F  +Q A+  AL  P   + EV+Q Y  RR+ L 
Sbjct: 246 RVGYMVGNKELCAALARIKSYHDYGTFTPIQVASVIALDGPQDCVEEVRQTYELRRNVLA 305

Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367
           +GL E GW V   KA+MY+W K P     +GS +FA  LL +  V V+PG  FG  G+ +
Sbjct: 306 KGLHEAGWMVEVPKASMYIWAKIPEPYAHLGSLEFAKKLLAEAKVAVSPGIGFGDYGDDH 365

Query: 368 VRISLIADCDRLGEALDRIK 387
           VR +LI +  R  +A+  IK
Sbjct: 366 VRFALIENEARTRQAIRGIK 385


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: 469
Number of extensions: 19
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: 395
Length adjustment: 31
Effective length of query: 372
Effective length of database: 364
Effective search space:   135408
Effective search space used:   135408
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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