Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_011799652.1 PNAP_RS01075 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000015505.1:WP_011799652.1 Length = 426 Score = 439 bits (1129), Expect = e-128 Identities = 228/431 (52%), Positives = 296/431 (68%), Gaps = 14/431 (3%) Query: 14 KPETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTD 73 K ETIA+HGG PDPTT + AVP+YQT +Y F +T H A LF L+ GNIY+R+MNPT Sbjct: 2 KIETIAVHGGYTPDPTTKAVAVPIYQTVAYAFDNTQHGADLFDLKVAGNIYSRIMNPTNA 61 Query: 74 VLEKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKL 133 VLE R+ ALEGG+ ALA ASG +A A+ I EAG IVASS+LYGGTYNL +TFP++ Sbjct: 62 VLEARMTALEGGIGALAVASGMAAIAYAIQTITEAGDNIVASSALYGGTYNLFAHTFPQM 121 Query: 134 GIKVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNT 193 GI+V F D DP +F + +T+A + E++GNP + DIAA++ VA GVPL++DNT Sbjct: 122 GIEVRFADPRDPGSFAPLIDARTKAVFCESVGNPLGNVTDIAALAGVAHAGGVPLIVDNT 181 Query: 194 MPSPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGK--FKNFTEPDPS 251 + SPYL P +HGADIVVH+LTK+LGGHGT++GG+I+D G F W K F+ EPD S Sbjct: 182 VSSPYLCRPFEHGADIVVHALTKYLGGHGTTLGGVIVDSGKFPWAEHKARFRRLNEPDVS 241 Query: 252 YHGLKFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMER 311 YHG+ + E G A+I +ARV LR++G A+S A+QILQG+ETL LRM+R Sbjct: 242 YHGVVYTEALGA--------AAYIGRARVVPLRNMGAALSAMAAFQILQGIETLALRMDR 293 Query: 312 HSGNALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKG---GVE 368 NAL +A FL+ HPK+ WVNY GL +++A ++Y G I+ F +K + Sbjct: 294 ICDNALAIAYFLKNHPKVAWVNYAGLPEHRDHALVQQY-MGGKASGIISFGVKSQADAMA 352 Query: 369 KAKKFIDGLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENI 428 +F D L+LF+ L NIGDAKSLA HPASTTH+QL E AGV+ VRLSVG+E+I Sbjct: 353 AGSRFQDALQLFTRLVNIGDAKSLACHPASTTHRQLNPAELAKAGVSTDMVRLSVGIEHI 412 Query: 429 DDILVDLEEAL 439 DD+L DLE+AL Sbjct: 413 DDLLADLEQAL 423 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: 503 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: 426 Length adjustment: 32 Effective length of query: 410 Effective length of database: 394 Effective search space: 161540 Effective search space used: 161540 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