Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_013553393.1 NITSA_RS02180 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q7M844 (422 letters) >NCBI__GCF_000186245.1:WP_013553393.1 Length = 421 Score = 547 bits (1409), Expect = e-160 Identities = 270/420 (64%), Positives = 331/420 (78%), Gaps = 1/420 (0%) Query: 1 MHPKTLAIQAGYEKGKGEKSIAVPIYQTTAYKFDDTEHGANLFDLKELGNIYTRIMNPTT 60 M TLAI AGY+ G ++AVPIYQTTAY+F D EH ANLF+LKELGNIYTR+MNPTT Sbjct: 1 MRENTLAIHAGYD-GNEFGTMAVPIYQTTAYEFRDAEHAANLFELKELGNIYTRLMNPTT 59 Query: 61 DVLEKRVALLEGGVAALASASGMASIFYAVANLAQSGENIIATTQLYGGTLNQFTHTLSR 120 DV EKR A LEGG AA+A+ASGM++IFYA+AN+A++G+NII Q+YGGT HT+ R Sbjct: 60 DVFEKRFAALEGGAAAVATASGMSAIFYAIANVAEAGDNIIVAKQVYGGTTTLTGHTIRR 119 Query: 121 FGIEVRFFDGNHPQEARALIDSKSRALFFESLTNPSIDVPEIDTLAKIADEYGIVSIVDN 180 FGIE R+FD P+E A+ID +++ + FES+TNPS+DV +I + +IAD +G+++ DN Sbjct: 120 FGIEARYFDVYEPEELEAMIDERTKLIHFESITNPSVDVADIAEIVRIADRHGVLTCTDN 179 Query: 181 TVATPAICRPIEHGVDVVVHSASKYMGGQGLAIGGVLVESARVAEKLRGNPRYPHFNTPD 240 TVATP IC+PIEHGVDVVVHSASKY GQGLAIGG++VE + EKL+GN RY HFN PD Sbjct: 180 TVATPVICKPIEHGVDVVVHSASKYTTGQGLAIGGIVVEREGLVEKLKGNQRYYHFNEPD 239 Query: 241 PSYHGLVYASAPLPPFVLRARLALLRDIGATLSPFDSWLFIQGIETLSVRMREHSLSAMK 300 PSYHGLVY PLPPF LR RLALLRD+GA SPF+SWL+IQG+ETL +RMR+HS SA+ Sbjct: 240 PSYHGLVYTDLPLPPFTLRTRLALLRDLGAAPSPFNSWLYIQGLETLPLRMRQHSDSALA 299 Query: 301 IAHYLQNHPKVQAVYYPGLESDKNHANAVKYFDEGMFSGLLSFEVGDFELAQKIADSVKI 360 IA +L+ HPKV+ V YPGL+SD N+ KYF +GM SGLLSFEV E AQ+IADS K+ Sbjct: 300 IAEFLEAHPKVKKVNYPGLKSDPNYPLVQKYFKKGMASGLLSFEVESREEAQRIADSTKL 359 Query: 361 FTLATNIGDTKSIITHSASTTHRQVSAEGLKKAGVTPGLVRLSIGLEDYRDLIEDLAQAI 420 F L NIGD+KS+ITH ASTTH+Q+S E L+ AGV GL+RLS+GLED DLIEDL QA+ Sbjct: 360 FKLVVNIGDSKSLITHPASTTHQQLSKEELEAAGVPEGLIRLSVGLEDTEDLIEDLRQAL 419 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: 579 Number of extensions: 17 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: 422 Length of database: 421 Length adjustment: 32 Effective length of query: 390 Effective length of database: 389 Effective search space: 151710 Effective search space used: 151710 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