GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Magnetospirillum magneticum AMB-1

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_011386083.1 AMB_RS18860 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q8YTF2
         (403 letters)



>NCBI__GCF_000009985.1:WP_011386083.1
          Length = 410

 Score =  333 bits (854), Expect = 5e-96
 Identities = 165/380 (43%), Positives = 241/380 (63%), Gaps = 3/380 (0%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           RI++LPPYVFA ++ +KA+AR  G D+ID GMGNPD  TP  +VD  ++A ++P+ H Y 
Sbjct: 9   RIKRLPPYVFAEVNAMKARARAAGEDIIDFGMGNPDQPTPAHIVDKLVEAARNPRAHRYS 68

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
              G    R+A++ +Y RR+ V +DP++E +  LGSKEGL++LA A  +PGD+VLVP+P+
Sbjct: 69  MSRGIPGLRKALSGYYQRRFAVDIDPETECIVTLGSKEGLANLANAITSPGDIVLVPNPS 128

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190
           YP H  G +IAGG+   + + P+ ++L  L         K   L  NYPSNPT   A  +
Sbjct: 129 YPIHPYGFIIAGGSCRFVPVTPDAEFLKALDRAVRHSVPKPIALVLNYPSNPTALLADLD 188

Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250
           F+ ++V F R + I ++ DL Y+E+ FD   P S+L+IPGAK+I VEF ++SKTYNM GW
Sbjct: 189 FYGQVVEFCRHHGIWILSDLAYSEIYFDVAPPPSILQIPGAKEIAVEFTSMSKTYNMPGW 248

Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310
           R+GF  GN+ +I  L  +K+ LDYG F  +Q AA  AL  P   + +++  Y+ RRD LI
Sbjct: 249 RIGFAAGNKTLIAALGRIKSYLDYGAFTPIQVAATAALNGPQDCVDDIRALYKGRRDALI 308

Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367
           +GL   GW++P   ATM+ W   P     +GS +F+  L+++  V V PG  FG  G+ +
Sbjct: 309 EGLSAAGWEIPSPPATMFAWAPIPKAFAHLGSLEFSKLLMREAQVAVAPGIGFGEYGDSH 368

Query: 368 VRISLIADCDRLGEALDRIK 387
           VRI L+ +  R  +A+  IK
Sbjct: 369 VRIGLVENVQRTRQAVRNIK 388


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: 484
Number of extensions: 25
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: 410
Length adjustment: 31
Effective length of query: 372
Effective length of database: 379
Effective search space:   140988
Effective search space used:   140988
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:

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