Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_011427595.1 RHE_RS22670 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::P74281 (384 letters) >NCBI__GCF_000092045.1:WP_011427595.1 Length = 364 Score = 134 bits (338), Expect = 3e-36 Identities = 100/336 (29%), Positives = 164/336 (48%), Gaps = 14/336 (4%) Query: 52 TENDVLMLTTSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEW 111 + NDVL++ T A+EA ++ PG L +G + + + G AV ++ A+ Sbjct: 33 SRNDVLLMQAEATVALEAVAVSLARPGLSALNVVTSSYGSWFGQWLRRGGAAVRDVAAQP 92 Query: 112 GKALDPNDFKTLLEA-DSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAV 170 G P + + + +A D+ + L + H+E+++G+LN L I A A+A G + +VDAV Sbjct: 93 GL---PIEIEAVAKALDAGPHVDLLAVVHAESASGILNPLTRIMALAQARG-IVTVVDAV 148 Query: 171 TSLGATPVAIDDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPR-FYLDLKK 229 S+G P+ ID LG+D+ G QK P G+ +SVS +AWQ PR L L Sbjct: 149 ASVGGHPLDIDGLGIDIAVIGPQKALGGPAGVSALSVSRRAWQLILRDGTPRDSILSLAD 208 Query: 230 YKKSTD--EDSSPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLP 287 K D P TP + L+A+L ++AEGL+++ RH +ATR + AL Sbjct: 209 LKTWVDGGRRGLPGTPSPLEFFALEATLDRIEAEGLESVIARHALAASATRTGLTALGAG 268 Query: 288 LFAPDNAASNAITAVAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLG-FVCD 346 + P ASN +T+VA T ++ + + G ++ R+ H G Sbjct: 269 AWVPSAKASNLVTSVAVPESLTPAALITTARRLGVELTEGVGTAPARLLRLNHTGPRAAF 328 Query: 347 RDILSCIGALEATLIELGYEGVTPGSGVAAAAGVLA 382 + +L+ + A A L + G+ S +AAAA ++ Sbjct: 329 QPVLANVAAFGAALRQAGHP-----SDIAAAAEAIS 359 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: 289 Number of extensions: 11 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: 364 Length adjustment: 30 Effective length of query: 354 Effective length of database: 334 Effective search space: 118236 Effective search space used: 118236 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 10 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