Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_004514406.1 GMET_RS04100 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase family protein
Query= BRENDA::Q187D4 (421 letters) >NCBI__GCF_000012925.1:WP_004514406.1 Length = 427 Score = 488 bits (1256), Expect = e-142 Identities = 224/415 (53%), Positives = 310/415 (74%) Query: 5 ETICVQGNYKPGNGEPRVLPLYQSTTFKYSSIDQLAELFDLKVDGHIYSRISNPTIQAFE 64 ET +QG Y P G+PRV+ + QSTTFKY + D + +LFDL+ G Y+R+ NPT AFE Sbjct: 8 ETQAIQGGYTPKAGDPRVVTICQSTTFKYDNADHVTKLFDLEEPGFFYTRLGNPTTDAFE 67 Query: 65 EKISLLEGGVSSVAVSSGQSANMLAVLNICKSGDSILCSSKVYGGTFNLLGPSLKKFGID 124 +K++++EGGV ++A S+GQ+A L++ NIC++G + +S +YGGT+NL +L K GI+ Sbjct: 68 QKLAMMEGGVGALATSAGQAATTLSIFNICQAGQHFVTASTLYGGTYNLFACTLPKMGIE 127 Query: 125 LISFDLDSSEDEIVELAKENTKVVFAETLANPTLEVIDFEKIANVAKRINVPFIVDNSLA 184 + D ++ DEI+ + NTK +FAET+ NP L V+DF K + +A+ VP I+D++ A Sbjct: 128 VSFVDPEAPADEILAAFRPNTKALFAETIGNPGLNVLDFAKFSAIAQEKGVPLIIDSTFA 187 Query: 185 SPVLCNPLKYGANIVTHSTTKYLDGHASSVGGIIVDGGNFNWDNGKFPELVEPDPTYHGI 244 +P LC P ++GAN+V HS TKY+DG A+SVGG+IVDGGNF+W NG+FPEL EPD +YHG+ Sbjct: 188 TPYLCRPFEHGANVVVHSATKYIDGLATSVGGVIVDGGNFDWGNGRFPELTEPDSSYHGL 247 Query: 245 SYTQKFGNAAYATKARVQLLRDYGNCLSPFNAYLTNLNVETLHLRMERHSENALKIARFL 304 Y + FGN AY KARVQL+RD G SPFN++L ++TL LRM+RHS+NAL +A+FL Sbjct: 248 QYVKTFGNLAYIIKARVQLMRDIGTTPSPFNSFLFTNGLQTLPLRMQRHSDNALALAQFL 307 Query: 305 EKHENVDWINYPGLEDNKYYENAKKYLSRGCSGVLSFGVRGGLENAKKFVEKLQIASLVT 364 E H +V W+ YPGL + ++ A+KYL +GCSGVL+FG++GG E KKF+E ++ +LV Sbjct: 308 ESHPSVSWVKYPGLSSHASHDRAQKYLPQGCSGVLTFGIKGGTEAGKKFMEACRLVALVV 367 Query: 365 HVSDVRTCVIHPASTTHRQLTEEQLIASGVLPSLIRLSVGIENVEDLIADLNQAL 419 HV D R+CV+HPASTTHRQLT EQ ASGV P LIRLSVGIE+++D+IAD++QAL Sbjct: 368 HVGDARSCVLHPASTTHRQLTAEQQTASGVTPDLIRLSVGIEHIDDIIADVDQAL 422 Lambda K H 0.316 0.135 0.387 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: 530 Number of extensions: 19 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: 421 Length of database: 427 Length adjustment: 32 Effective length of query: 389 Effective length of database: 395 Effective search space: 153655 Effective search space used: 153655 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 Jul 25 2024. The underlying query database was built on Jul 25 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