Align Phosphoserine aminotransferase; EC 2.6.1.52 (characterized, see rationale)
to candidate WP_012503202.1 CPAR_RS10040 alanine--glyoxylate aminotransferase family protein
Query= uniprot:F9VNX9 (372 letters) >NCBI__GCF_000020505.1:WP_012503202.1 Length = 379 Score = 144 bits (363), Expect = 4e-39 Identities = 103/338 (30%), Positives = 165/338 (48%), Gaps = 8/338 (2%) Query: 2 LLIPGPVEVPRSVR-EASTLVVNHRSEKFREIVRKLESLMNKHFSASR-TALLTGSGTLA 59 L PGP VP +V + +++HR+ +F EI+ ++ + F ++ ++T SGT Sbjct: 5 LFTPGPTPVPENVMLRMAAPIIHHRNPEFMEILERVHQDLQYLFRTTQPVVVMTCSGTGG 64 Query: 60 VEAMVYSLIKPNEKVISFPYGEFGNRLVDSLRRRGAQVKVYEKKIGEIFSIDEIKKALDE 119 +EA + SL +KVI+ G+FG R + R + G + + + + L E Sbjct: 65 MEAAISSLFTRGDKVITVNGGKFGERWGELARIFTGNCVEEKVAWGSAITTERMVELLKE 124 Query: 120 NKDATAVALVHNETSSGMAFRNLEDVVSEVKRRGLKLLVDSVSGFAAYKLLVNEWKIDAV 179 + A V + H+ETS+G A + + +LVD ++ A++ ++W D Sbjct: 125 HPGAMGVCITHSETSTGTASDVKALCAAIHEHSDALILVDGITAIGAHEFRFDDWGADIC 184 Query: 180 ATGSQKALASVPGMSFVALSDDGIEEIQG-ESLPSY-LDISLHLKFQDKGETPFTPAVGV 237 TGSQK L PG++ VA+S+ + I + LP Y L + LK +TPFTPAV + Sbjct: 185 ITGSQKGLMMPPGLALVAISERAQDVINNRKGLPQYYLSLKKALKSHAGNDTPFTPAVSL 244 Query: 238 FNASLRAAELLEIEGIENRWKRHEACARFVREVLSSYGFLLFGNENNFSNTVVAGVPPIP 297 A +++ EGIEN WKRHE A R + G LF +++ T V +P Sbjct: 245 IIGLDEALQMVRAEGIENVWKRHEQLAEACRLGCQALGMELFSESPSYAVTAV-WLPEGA 303 Query: 298 DYRK---KLLNEFNIEISGGMGELKEKIVRIGLLGVVD 332 D+++ L E I ++ G + K KI RI LG D Sbjct: 304 DWKQFNNTLKIENGITVAAGQDDFKGKIFRISHLGYYD 341 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: 289 Number of extensions: 15 Number of successful extensions: 4 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: 379 Length adjustment: 30 Effective length of query: 342 Effective length of database: 349 Effective search space: 119358 Effective search space used: 119358 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 25 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