Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_004312943.1 C665_RS12780 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000310185.1:WP_004312943.1 Length = 423 Score = 472 bits (1215), Expect = e-138 Identities = 241/428 (56%), Positives = 304/428 (71%), Gaps = 11/428 (2%) Query: 14 KPETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTD 73 K ETIA+HGG PDPTT + AVP+YQTTSY F DT H A LF L+ GNIYTR+MNPTT Sbjct: 2 KLETIAVHGGYSPDPTTKAVAVPIYQTTSYAFDDTQHGADLFDLKVQGNIYTRIMNPTTA 61 Query: 74 VLEKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKL 133 VLE+RVA LEGG+ ALA ASG SA A+ I EAG IV++S+LYGGTYNL +TFP+ Sbjct: 62 VLEQRVAQLEGGIGALAVASGMSAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTFPQF 121 Query: 134 GIKVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNT 193 GI+V F D DP++F + +T+A Y E++GNP + DI ++++A + GVPL++DNT Sbjct: 122 GIEVRFADYRDPDSFAALIDARTKAIYCESVGNPLGNVTDIGRLAEIAHKAGVPLIVDNT 181 Query: 194 MPSPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGK--FKNFTEPDPS 251 +PSPYL P +HGADIVVH+LTK+LGGHG SIGG+I+D G F W K FK EPD S Sbjct: 182 VPSPYLCRPFEHGADIVVHALTKYLGGHGNSIGGVIVDSGKFPWAEHKARFKRLNEPDVS 241 Query: 252 YHGLKFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMER 311 YHG+ + E G AFI +ARV LR+ G AISPFN++ ILQG+ETL LRM+R Sbjct: 242 YHGVCYTEALGA--------AAFIGRARVVPLRNTGAAISPFNSFLILQGIETLALRMDR 293 Query: 312 HSGNALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAK 371 N +KVAE+L+KH K+EWVNY GL ++A +KY G I+ F +KGG E Sbjct: 294 ICTNTIKVAEYLKKHAKVEWVNYAGLPDHADHALVQKY-MGGRASGILSFGVKGGFEAGG 352 Query: 372 KFIDGLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDI 431 +F D L+L + L NIGDAKSLA HPASTTH+QL+ E AGV+P VRLS+G+E+IDDI Sbjct: 353 RFQDALKLITRLVNIGDAKSLACHPASTTHRQLSPAELAKAGVSPDMVRLSIGIEHIDDI 412 Query: 432 LVDLEEAL 439 + DLE+AL Sbjct: 413 VADLEQAL 420 Lambda K H 0.317 0.137 0.402 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: 531 Number of extensions: 14 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: 442 Length of database: 423 Length adjustment: 32 Effective length of query: 410 Effective length of database: 391 Effective search space: 160310 Effective search space used: 160310 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: 51 (24.3 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