Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_011841308.1 RSPH17029_RS09535 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000015985.1:WP_011841308.1 Length = 400 Score = 169 bits (428), Expect = 1e-46 Identities = 124/386 (32%), Positives = 181/386 (46%), Gaps = 17/386 (4%) Query: 7 LMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSGTGA 66 L IPGP+ +P++VL AM + G +++A L +LK + TE+ V + +G GA Sbjct: 10 LAIPGPSAMPDRVLNAMHRAAPNIYEGALHEMVASLWPDLKRIAGTEHQVALYIANGHGA 69 Query: 67 MEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTLLEA 126 EA+ N S GDR LV G+FG W + A+ G+ V+ I DP + L A Sbjct: 70 WEAANANLFSRGDRALVLATGRFGHGWAESARALGVDVQLIDFGRAAPADPARLEEALRA 129 Query: 127 DSDKTIKALIITHSETSTGVLNDLAAINAAAKAHG-GALMIVDAVTSLGATPVAIDDLGL 185 D IKA+++TH +T+T + ND+AA+ AA A G AL+ VD + SL +D+ G Sbjct: 130 DPGHRIKAVLVTHVDTATSIRNDVAALRAAIDAVGHPALLAVDCIASLACDEYRMDEWGA 189 Query: 186 DVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTD-EDSSPFTPP 244 DV SQKG M PPGLGFV S +A + + + Y D T+ T P Sbjct: 190 DVTVGASQKGLMTPPGLGFVWYSDRALERCRASDLRTPYWDWTPRSFGTEFWQHFCGTAP 249 Query: 245 INLMYGLQASLQMMKAEGLDAIFTRHQRHTNAT-----RGAMKALNLPLFAPDNAASNAI 299 + +YGL+A+L M+ EGL A++ RH+ A R + L D A Sbjct: 250 THHLYGLRAALDMILEEGLPAVWARHEALARAVWTAFDRWGAGNPEIALNVADAACRGRS 309 Query: 300 TAVAPLGV-------EAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSC 352 A +G E + R+ + + MA + R+ H+G V L Sbjct: 310 VTAARMGAPHATRLREWTETRAGVTLGIGLGMALPSEPAYHGFLRVAHMGHVNAHMTLGA 369 Query: 353 IGALEATLIELGYEGVTPGSGVAAAA 378 + +EA L L + G G AAA Sbjct: 370 LAVMEAGLAAL---EIPHGEGALAAA 392 Lambda K H 0.317 0.134 0.386 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: 318 Number of extensions: 13 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: 384 Length of database: 400 Length adjustment: 31 Effective length of query: 353 Effective length of database: 369 Effective search space: 130257 Effective search space used: 130257 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 16 2024. The underlying query database was built on Apr 09 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