GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Thiohalospira halophila DSM 15071 HL 3

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_093427016.1 BM272_RS01690 alanine transaminase

Query= BRENDA::Q8YTF2
         (403 letters)



>NCBI__GCF_900112605.1:WP_093427016.1
          Length = 397

 Score =  352 bits (903), Expect = e-101
 Identities = 175/380 (46%), Positives = 245/380 (64%), Gaps = 3/380 (0%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           RI++LPPYVF  +++LKAKAR +G D++D GMGNPD  TP+ +VD  ++A Q    H Y 
Sbjct: 7   RIKRLPPYVFNIVNDLKAKARARGEDIVDFGMGNPDQPTPRHIVDKLVEAAQRNNTHRYS 66

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
              G    RRAI+ WY  RY V +DP++EA+  +GSKEGL+HLA++ +  GD VLVP+PA
Sbjct: 67  VSRGIPRLRRAISQWYADRYDVAIDPENEAIVTIGSKEGLAHLALSVLEQGDTVLVPNPA 126

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190
           YP H  G VIAG  +  + L P+ D+  +L    +E   + K+L  N+P NPT      +
Sbjct: 127 YPIHPYGVVIAGADIRHVPLVPDVDFFAELERAIKEAWPRPKMLILNFPGNPTTQCVDLD 186

Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250
           FFE +VA AR+Y I +VHD+ YAE+ FDGY+  S+L++PGAK++ VEF++LSKTYNM GW
Sbjct: 187 FFEHVVAMAREYGIWVVHDIAYAEITFDGYEAPSILQVPGAKEVAVEFYSLSKTYNMPGW 246

Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310
           RVGF+ GN  ++  L  +K+ LDYG F  +Q AA  AL+ P     E++  Y  RRD L+
Sbjct: 247 RVGFMCGNDKLVAALARMKSYLDYGTFTPIQVAAIHALEGPQECKEEIRAMYERRRDHLV 306

Query: 311 QGLGELGWDVPKTKATMYLWVKCPVG---MGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367
            GL   GW+V   +ATM++W   P     +GS +F+  LLQ   V V+PG  FG  G+ +
Sbjct: 307 SGLRGAGWEVESPRATMFVWAPIPEAYRHLGSLEFSKKLLQDAKVAVSPGIGFGEYGDDH 366

Query: 368 VRISLIADCDRLGEALDRIK 387
           VR SLI +  R  +A+  I+
Sbjct: 367 VRFSLIENEHRTRQAVRGIR 386


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: 477
Number of extensions: 23
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: 397
Length adjustment: 31
Effective length of query: 372
Effective length of database: 366
Effective search space:   136152
Effective search space used:   136152
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 Jul 25 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