Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_011952121.1 SWIT_RS06485 O-acetylhomoserine aminocarboxypropyltransferase
Query= metacyc::MONOMER-17873 (438 letters) >NCBI__GCF_000016765.1:WP_011952121.1 Length = 431 Score = 582 bits (1499), Expect = e-170 Identities = 290/423 (68%), Positives = 333/423 (78%), Gaps = 1/423 (0%) Query: 13 YHQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEEIGFAYTRIGNPT 72 Y +TLALH G +RADPTTGAVA PIYQTTSYQ HD HAARL LEE+G YTRIGNPT Sbjct: 6 YRPETLALHAG-WRADPTTGAVAPPIYQTTSYQFHDAGHAARLFALEELGNIYTRIGNPT 64 Query: 73 QDAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLYGGTWNLFANTLR 132 E R+AALEGG AALA+ASGQAASA A+ LA+AGDNIV T LYGGTWNLFANTLR Sbjct: 65 TAILEDRIAALEGGAAALAVASGQAASAYAIQNLARAGDNIVAGTHLYGGTWNLFANTLR 124 Query: 133 TLGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAAIGRSLGVPLIID 192 GIE RFVDPADP+ F A+D RTR +Y ETLPNPKL V PIAE+AA GR +G+PLI+D Sbjct: 125 DQGIEVRFVDPADPQGFVAASDDRTRAWYVETLPNPKLVVCPIAELAAAGRPIGIPLIVD 184 Query: 193 NTATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADHAERHALLTGPEP 252 NTA PLIARP DHGAA+VVYSTTKYIGGHGT+IGG I+DGG F W +R L P+P Sbjct: 185 NTAAPLIARPLDHGAAIVVYSTTKYIGGHGTSIGGVIVDGGNFDWEAFPDRQPNLNTPDP 244 Query: 253 SYHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLETLPLRLARHNAN 312 SYH A W A P GP+AYILRAR +LRDLGA+++P +AF ++QGLETLPLR+ RH N Sbjct: 245 SYHGAVWAQAAKPLGPIAYILRARTILLRDLGAALSPFNAFQILQGLETLPLRMPRHCEN 304 Query: 313 AIKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELAGGEEAGRRFIEA 372 A+ V +L+ V+ V P +Q+GE R RAD L GG GGL+GFELAGG EAGRRFI+A Sbjct: 305 ALAVVRFLSGRADVTRVIHPSVQTGEERARADRVLTGGQGGLLGFELAGGVEAGRRFIDA 364 Query: 373 LRLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIGIEHPDDIIGDIA 432 LRLFYHV NIGDARSLAIHPA+TTHSQLS E+Q A GV+PG+VRLSIG+EH DDI+ D+ Sbjct: 365 LRLFYHVANIGDARSLAIHPASTTHSQLSAEEQAAAGVSPGYVRLSIGLEHIDDILADLD 424 Query: 433 QAL 435 QAL Sbjct: 425 QAL 427 Lambda K H 0.319 0.136 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: 649 Number of extensions: 23 Number of successful extensions: 1 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: 438 Length of database: 431 Length adjustment: 32 Effective length of query: 406 Effective length of database: 399 Effective search space: 161994 Effective search space used: 161994 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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