Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate GFF2363 PGA1_c23940 putative serine-glyoxylate aminotransferase
Query= BRENDA::P74281 (384 letters) >FitnessBrowser__Phaeo:GFF2363 Length = 421 Score = 178 bits (452), Expect = 2e-49 Identities = 125/393 (31%), Positives = 207/393 (52%), Gaps = 20/393 (5%) Query: 7 LMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSGTGA 66 L IPGP+ +P+ VL AM + +G+ ++ A L +L+ + +TE++V + ++G GA Sbjct: 14 LAIPGPSVIPDAVLQAMHRPSPNIYAGELVEMTATLIPDLRRVARTEHNVAIYISNGHGA 73 Query: 67 MEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTLLEA 126 EA++ N L PGD VLV ++G+F W ++A+ G+ VE + G D + + L A Sbjct: 74 WEAALQNTLQPGDTVLVASSGRFAIGWSEMAEALGIKVELLDFGTGAPWDMDRIASHLAA 133 Query: 127 DSDKTIKALIITHSETSTGVLNDLAAINAAAKA-HGGALMIVDAVTSLGATPVAIDDLGL 185 D+ IKA++ H +TS+ + ND+AA+ AA A AL++ D + SLG +D G+ Sbjct: 134 DTAHRIKAVLAVHVDTSSSIRNDVAAMRAALDACDHPALLMADCIASLGCDRFEMDAWGV 193 Query: 186 DVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPF---T 242 DV+ + QKG M+P G+GFV S KA +A A +PR ++ E+ + T Sbjct: 194 DVMVAACQKGLMVPAGMGFVFFSPKAAEA--RARLPRVSRYWDWEPRANPEEFYQYFGGT 251 Query: 243 PPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALN----LPLFAPDNA-ASN 297 P + +YGL+A+L ++ EG++A++ RH R A A L + D A SN Sbjct: 252 APTHHLYGLRAALDLIHGEGMEAVWARHHRLAQAIWAACDRWGDGGPLRMNVQDVALRSN 311 Query: 298 AITAVAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGK------IFRIGHLGFVCDRDILS 351 A+T++ G EA ++R+ + + + + G R+GH+G V + I+ Sbjct: 312 AVTSLHLGGDEATRLRTWVEQTLGLTLGIGLGMAPPNSPEWHGFLRLGHMGHVSGQMIMG 371 Query: 352 CIGALEATLIELGYEGVTPGSGVAAAAGVLAKG 384 +G ++A L L + GSG AA + G Sbjct: 372 LLGGVDAGLKAL---EIPHGSGALEAASQVIAG 401 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: 373 Number of extensions: 22 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: 384 Length of database: 421 Length adjustment: 31 Effective length of query: 353 Effective length of database: 390 Effective search space: 137670 Effective search space used: 137670 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 09 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