Align Phosphoserine aminotransferase; EC 2.6.1.52 (characterized, see rationale)
to candidate WP_085635109.1 MGEO_RS02560 2-aminoethylphosphonate--pyruvate transaminase
Query= uniprot:F9VNX9 (372 letters) >NCBI__GCF_002115805.1:WP_085635109.1 Length = 393 Score = 100 bits (248), Expect = 9e-26 Identities = 104/374 (27%), Positives = 156/374 (41%), Gaps = 14/374 (3%) Query: 2 LLIPGPVEVPRSVREASTLVVNHRSEKFREIVRKLES----LMNKHFSASRTALLTGSGT 57 LL PGP+ SV++A + FR + R L S L+ S + GSG+ Sbjct: 16 LLTPGPLTTAYSVKQAMLKDWGSWDDDFRAMTRALRSRLLALIGGGASDYDCVPIQGSGS 75 Query: 58 LAVEAMVYSLIKPNEKVISFPYGEFGNRLVDSLRRRGAQVKVYEKKIGEIFSIDEIKKAL 117 VEAM+ S + + KV+ G +G R +L + +K DE+ L Sbjct: 76 YCVEAMLGSFVPRDGKVLVLANGAYGLRAAQTLGYLERDYHLLDKGDYLPPRGDEVAAIL 135 Query: 118 DENKDATAVALVHNETSSGMAFRNLEDVVSEVKRRGLKLLVDSVSGFAAYKLLVNEWKID 177 + T V +H ETSSG+ +E++ K G KLL+DS+S F A L + Sbjct: 136 AADPAITHVLAIHCETSSGIQ-NPVEEIAEATKAAGRKLLIDSMSAFGALPLDPVKLNCA 194 Query: 178 AVATGSQKALASVPGMSFVALSDDGIEEIQGESLPSYLDISLHLKFQDK-GETPFTPAVG 236 A + + K + VPG FV D IE +G S LD+ +K G+ FTP Sbjct: 195 AFVSSANKCIEGVPGFGFVIARKDEIEASKGNSHSLSLDVHAQWATMEKTGQWRFTPPTH 254 Query: 237 VFNASLRAAELLEIE-GIENRWKRHEACARFVREVLSSYGFLLFGNENNFSNTVVAGVPP 295 V A L+A +L E E G+ R R+ V + + GF + S +V P Sbjct: 255 VVAAFLKALDLHEAEGGVSARGARYTRNRDVVVQGMRDLGFETLLADRWLSPIIVTFFCP 314 Query: 296 IPDYRKKLLNEFNIEISGGMGELKEKIV-----RIGLLGVVDSRAVNKLLEATA-KLLDK 349 D ++ + G K+ RIG++G +D + +++EA L D Sbjct: 315 -ADPSFTFQGFYDAMKARGFIIYPGKLTVVNSFRIGVIGQMDEHVMRRVVEAARDALTDM 373 Query: 350 NYDYLPPRECKLPE 363 N P L E Sbjct: 374 NVSSAAPPAAALEE 387 Lambda K H 0.316 0.135 0.377 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: 301 Number of extensions: 16 Number of successful extensions: 3 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: 372 Length of database: 393 Length adjustment: 30 Effective length of query: 342 Effective length of database: 363 Effective search space: 124146 Effective search space used: 124146 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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:
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