Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_028490078.1 Q394_RS0115620 alanine--glyoxylate aminotransferase family protein
Query= metacyc::MONOMER-15919 (385 letters) >NCBI__GCF_000621325.1:WP_028490078.1 Length = 393 Score = 221 bits (563), Expect = 3e-62 Identities = 132/375 (35%), Positives = 208/375 (55%), Gaps = 6/375 (1%) Query: 8 KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66 + LM PGP+ V P VL AMA P +GH + N++++ L+ F T+N+ T ++ G Sbjct: 11 RTLMGPGPSDVSPRVLGAMARPTVGHLDPAFVNMMDEVKAMLQYAFQTKNELTMAVSAPG 70 Query: 67 TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126 +A M+ N+++ GDKV+ G FG R V+ I + +WG +P V+ Sbjct: 71 SAGMETCFVNLVEPGDKVIVCQNGVFGGRMKENVERCGATPIMVMDDWGKPVDPNKVEAA 130 Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186 L D K V VH ETSTGA++ + + ++ D+D L IVD V+SL G + +D++ ID Sbjct: 131 LKANPDAKVVAFVHAETSTGAQSDAQTLVKLAHDHDCLTIVDAVTSLAGTPLKMDEWGID 190 Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYY--EEKKQTPY 243 +G+QKCL+ PG++ ++ ++A E IK V +++D+ Y+ K+ + Sbjct: 191 AIYSGTQKCLSCVPGISPVSFGDRAIERIKNRKTTVQSWFMDMNLVMAYWGGTGKRAYHH 250 Query: 244 TPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTS 303 T +VN YAL+ +L ++ EEG+EN RH R +A +AG+EAMG+ E R + S Sbjct: 251 TAAVNTLYALHESLVMLQEEGLENSWARHARNHQALKAGIEAMGLRFVVDEPYRLPQLNS 310 Query: 304 AKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGIC-GEKEVLATLACVELA 362 PEG++++ R L N Y++ + G LAGKI+RIG MG EK VL L ++ Sbjct: 311 VTLPEGVDEAAVRTALLNDYSLEIGAGLGALAGKIWRIGLMGFASNEKNVLNCLGALDAV 370 Query: 363 LKELGFEVKESGVEV 377 L + ++ SGV V Sbjct: 371 LSGMNAQI-NSGVAV 384 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: 334 Number of extensions: 12 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 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