Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_011159786.1 TX73_RS21680 O-acetylhomoserine aminocarboxypropyltransferase
Query= metacyc::MONOMER-17873 (438 letters) >NCBI__GCF_000195775.1:WP_011159786.1 Length = 435 Score = 590 bits (1522), Expect = e-173 Identities = 285/422 (67%), Positives = 341/422 (80%), Gaps = 1/422 (0%) Query: 14 HQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEEIGFAYTRIGNPTQ 73 H +TLALH G +RADP+TG+VAVP++QTTSYQ H+T HAA L L+E+G YTRIGNPT Sbjct: 6 HPETLALHAG-WRADPSTGSVAVPLFQTTSYQFHNTEHAANLFALKELGNIYTRIGNPTT 64 Query: 74 DAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLYGGTWNLFANTLRT 133 D EQR+AALEGGVAALA+ASGQAASA A+ LA+ GDN+V+STDLYGGTWNLFANTL+ Sbjct: 65 DVLEQRVAALEGGVAALAVASGQAASAFALQNLARVGDNVVSSTDLYGGTWNLFANTLKD 124 Query: 134 LGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAAIGRSLGVPLIIDN 193 GIE RFVDP+DP+AF RATD RTR YY ETLPNPKL VFPI EVAAIGR G+PLI+DN Sbjct: 125 QGIEVRFVDPSDPQAFERATDERTRAYYAETLPNPKLAVFPIEEVAAIGRKHGIPLIVDN 184 Query: 194 TATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADHAERHALLTGPEPS 253 TA PL+ +P +HGAA+VVYS TKY+GGHGT+IGG I+DGG FPW +R +L P+PS Sbjct: 185 TAAPLLVKPLEHGAAIVVYSATKYLGGHGTSIGGLIVDGGNFPWEQFPQRQPVLNTPDPS 244 Query: 254 YHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLETLPLRLARHNANA 313 YH A W + P GP+AYI++AR +LRDLG++++P +AF +IQGLETLPLR+ RH NA Sbjct: 245 YHGAVWVEAVKPIGPVAYIIKARTTLLRDLGSALSPFNAFQIIQGLETLPLRIERHVQNA 304 Query: 314 IKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELAGGEEAGRRFIEAL 373 KVADYL P+V V P QSG AR RA+ YL+G +GGL+GFELAGG EAGR+FI+AL Sbjct: 305 QKVADYLEKRPEVVKVIHPSKQSGVARERAEKYLQGKFGGLVGFELAGGREAGRKFIDAL 364 Query: 374 RLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIGIEHPDDIIGDIAQ 433 L YHV NIGDARSLAIHPA+TTHSQLS E+Q ATGV+ G+VRLSIG+EH DDI+ DI + Sbjct: 365 ELLYHVANIGDARSLAIHPASTTHSQLSTEEQLATGVSDGYVRLSIGLEHIDDILADIDR 424 Query: 434 AL 435 L Sbjct: 425 GL 426 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: 618 Number of extensions: 15 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: 435 Length adjustment: 32 Effective length of query: 406 Effective length of database: 403 Effective search space: 163618 Effective search space used: 163618 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