Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_007472892.1 CMTB2_RS00355 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q7M844 (422 letters) >NCBI__GCF_000170735.1:WP_007472892.1 Length = 418 Score = 451 bits (1159), Expect = e-131 Identities = 220/421 (52%), Positives = 311/421 (73%), Gaps = 4/421 (0%) Query: 1 MHPKTLAIQAGYEKGKGEKSIAVPIYQTTAYKFDDTEHGANLFDLKELGNIYTRIMNPTT 60 M TLA+ GYEK K EK++ VPIY ++AY++ DT+H A LF+L+E GNIYTRI NPTT Sbjct: 1 MKDSTLALHYGYEKDK-EKTMQVPIYMSSAYEYQDTDHAARLFNLQEEGNIYTRIGNPTT 59 Query: 61 DVLEKRVALLEGGVAALASASGMASIFYAVANLAQSGENIIATTQLYGGTLNQFTHTLSR 120 V EKR+A LE G+ ALA+ASGM++IFY++ANL ++G+N+I + +LYGG++ T TL + Sbjct: 60 RVFEKRIAALENGIDALATASGMSAIFYSIANLVKNGDNVIISNKLYGGSITLSTQTLKQ 119 Query: 121 FGIEVRFFDGNHPQEARALIDSKSRALFFESLTNPSIDVPEIDTLAKIADEYGIVSIVDN 180 FGI+ ++FD +P+ LID ++A+ FES+ NP+++V + + +++IA++ GI++I DN Sbjct: 120 FGIKAKYFDIKNPEMLEELIDENTKAILFESIANPALNVADFEIISEIANKRGIITICDN 179 Query: 181 TVATPAICRPIEHGVDVVVHSASKYMGGQGLAIGGVLVESARVAEKLRGNPRYPHFNTPD 240 T+ATP +PI G+D+VVHSASKY+ G G IGG ++ES EKL+G+ RYP FN PD Sbjct: 180 TIATPYSLKPINLGIDIVVHSASKYLSGNGTVIGGCIIESKSAKEKLKGD-RYPQFNKPD 238 Query: 241 PSYHGLVYASAPLPPFVLRARLALLRDIGATLSPFDSWLFIQGIETLSVRMREHSLSAMK 300 SYHGL+Y PF+ R+RLALLRD GA +SPF+SWL I G+ETL +R+ HS +A++ Sbjct: 239 DSYHGLIYNEKFDNPFIARSRLALLRDYGAVISPFNSWLLILGLETLHLRIERHSYNALE 298 Query: 301 IAHYLQNHPKVQAVYYPGLESDKNHANAVKYFDEGMFSGLLSFEVGDFELAQKIADSVKI 360 IA +L +H KV+ V YP L +D+N+ A KY G SG+LSFE+ +E A+ +KI Sbjct: 299 IAKFLSSHKKVKKVSYPFLNNDENYNLAKKYLKYG--SGILSFELSSYEEAKNFVKKLKI 356 Query: 361 FTLATNIGDTKSIITHSASTTHRQVSAEGLKKAGVTPGLVRLSIGLEDYRDLIEDLAQAI 420 F L TNI DTKSI+TH ASTTH+Q++ E LK AG++ GL+RLS+G+ED DLI+DL +A+ Sbjct: 357 FKLVTNIADTKSIVTHPASTTHQQLNKEELKNAGISEGLIRLSVGIEDVEDLIKDLDEAL 416 Query: 421 D 421 + Sbjct: 417 N 417 Lambda K H 0.318 0.135 0.385 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: 504 Number of extensions: 25 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: 422 Length of database: 418 Length adjustment: 32 Effective length of query: 390 Effective length of database: 386 Effective search space: 150540 Effective search space used: 150540 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 (21.7 bits) S2: 50 (23.9 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