Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 3609101 Dshi_2489 Serine--glyoxylate transaminase (RefSeq)
Query= BRENDA::P74281 (384 letters) >FitnessBrowser__Dino:3609101 Length = 400 Score = 238 bits (607), Expect = 2e-67 Identities = 143/375 (38%), Positives = 209/375 (55%), Gaps = 5/375 (1%) Query: 7 LMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTT-SGTG 65 L IPGPT VPE V AM R+ DF + L +K + +TE +ML SGTG Sbjct: 8 LFIPGPTNVPEAVRQAMNVPMQDMRAADFGDLTLGLFEGMKSVLRTERGTVMLFPGSGTG 67 Query: 66 AMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFKTLLE 125 A EA+I N L+PGD+VL+ +G F W ++A+ GL VE I WG + L Sbjct: 68 AWEAAITNTLNPGDKVLMARHGHFSTLWAQMAERLGLQVELIDIPWGAGAPVKEIARRLG 127 Query: 126 ADSDKTIKALIITHSETSTGVLNDLAAINAAAKAH-GGALMIVDAVTSLGATPVAIDDLG 184 D+ IKA+ +TH+ET+TGV +D+AA+ A + AL+ VD V+S+G+ +D+ Sbjct: 128 RDAHDEIKAVFVTHNETATGVASDIAAVRRALDENFHDALLFVDGVSSVGSLDFRMDEWE 187 Query: 185 LDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSPFTPP 244 +D+V +GSQKG M+PPGLG + VS KA +A +AT+ R Y + + P+TPP Sbjct: 188 VDLVVTGSQKGLMLPPGLGILGVSEKALEAARSATMRRAYFEFSDMLAMNADGYFPYTPP 247 Query: 245 INLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAA-SNAITAV- 302 L++GL+ASL + EGLD + RH R R + A LPL A + S+ ++A+ Sbjct: 248 TPLLHGLRASLARIATEGLDNVIARHTRLAEGVRRGIAAWGLPLVAEHHTLYSDTVSAIR 307 Query: 303 APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEATLIE 362 P ++A ++ ++F+ + G L GK+FRIGHLG + + L+ + E L Sbjct: 308 VPQEIDAREVLRIAYEEFNTSFGSGLGPLDGKVFRIGHLGDLNEAMCLTALSVAEMALYR 367 Query: 363 LGYEGVTPGSGVAAA 377 G + V GSGV AA Sbjct: 368 AGMQ-VQLGSGVGAA 381 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: 325 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: 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 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