Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_026185995.1 THITHI_RS0102480 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000378965.1:WP_026185995.1 Length = 393 Score = 220 bits (561), Expect = 5e-62 Identities = 134/376 (35%), Positives = 205/376 (54%), Gaps = 5/376 (1%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 + LM PGP+ V P VL AMA P IGH + +++++ L+ F TEN T ++ G Sbjct: 11 RTLMGPGPSDVNPRVLAAMARPTIGHLDPVFVDMMDEMKGLLQYAFQTENQLTLPVSAPG 70 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 +A M+M N+++ GD V+ + G FG R V+ A+ ++ EWG +P ++E Sbjct: 71 SAGMEMCFVNLVEPGDTVVVCINGVFGGRMKENVERCGATAVVVEDEWGKPVDPGKLEEA 130 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 L + + V VH ETSTGA + K + E+ +D L IVD+V+ LGG + VD + ID Sbjct: 131 LKAHPEAGVVAFVHAETSTGACSDAKALTEIAHRHDCLVIVDSVTGLGGVELRVDDWGID 190 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEE--KKQTPY 243 +GSQKCL+ PGL+ ++ SE+A IK KV ++LDL Y+ K+ + Sbjct: 191 AIYSGSQKCLSCTPGLSPVSFSERAVARIKGRSHKVQSWFLDLNLVMGYWGSGTKRAYHH 250 Query: 244 TPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTS 303 T +N YAL+ +L ++ EEG+EN RH +A +AGLE+MG+ L +R + + Sbjct: 251 TAPINALYALHESLVILQEEGLENAWARHRAHHEALKAGLESMGLNLIVPRDSRLPQLNA 310 Query: 304 AKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGI-CGEKEVLATLACVELA 362 P G++++ R L + Y + + G LAGK++RIG MG K VL L +E Sbjct: 311 VSVPAGVDEAAVRKALLDDYGLEIGAGLGPLAGKVWRIGLMGFGANRKNVLLCLGALENT 370 Query: 363 LKELGFEVKESGVEVA 378 L G +V+ G A Sbjct: 371 LAGQGTDVRAGGAVAA 386 Lambda K H 0.316 0.135 0.379 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: 376 Number of extensions: 14 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: 385 Length of database: 393 Length adjustment: 30 Effective length of query: 355 Effective length of database: 363 Effective search space: 128865 Effective search space used: 128865 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