Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_084276346.1 B8779_RS08950 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q7M844 (422 letters) >NCBI__GCF_900176045.1:WP_084276346.1 Length = 419 Score = 536 bits (1382), Expect = e-157 Identities = 269/421 (63%), Positives = 335/421 (79%), Gaps = 2/421 (0%) Query: 1 MHPKTLAIQAGYEKGKGEKSIAVPIYQTTAYKFDDTEHGANLFDLKELGNIYTRIMNPTT 60 M +T+A+ AGYEK + +K++AVPIY TTAY FD EH ANLF LKELGNIYTRI NPTT Sbjct: 1 MKKETIALHAGYEKDE-QKTMAVPIYMTTAYAFDSAEHAANLFALKELGNIYTRIGNPTT 59 Query: 61 DVLEKRVALLEGGVAALASASGMASIFYAVANLAQSGENIIATTQLYGGTLNQFTHTLSR 120 DV EKR A LEGGVAALA++SGMA+I Y++ NL ++G+NIIA QLYGGT+ FTHTL R Sbjct: 60 DVFEKRFAALEGGVAALATSSGMAAINYSILNLCETGDNIIAANQLYGGTVTLFTHTLKR 119 Query: 121 FGIEVRFFDGNHPQEARALIDSKSRALFFESLTNPSIDVPEIDTLAKIADEYGIVSIVDN 180 GIE R FD + P+ LID K++A+FFES+TNPSIDVP+ + + IA ++ I++IVDN Sbjct: 120 LGIEARMFDVHKPELIEKLIDEKTKAIFFESITNPSIDVPDFEKIVAIAKKHNILTIVDN 179 Query: 181 TVATPAICRPIEHGVDVVVHSASKYMGGQGLAIGGVLVESARVAEKLRGNPRYPHFNTPD 240 TVATP +C PIE+GVDVVVHS SKY GQGLA+GG++VE+ EK++ N RY HFN PD Sbjct: 180 TVATPILCNPIEYGVDVVVHSTSKYTTGQGLALGGIIVEAESAKEKIKNNSRYNHFNEPD 239 Query: 241 PSYHGLVYASAPLPPFVLRARLALLRDIGATLSPFDSWLFIQGIETLSVRMREHSLSAMK 300 SYHGLVY+ P PPF+LRARL+LLRD+G+ SPF+SWLFIQG+E L++R+++HS SA++ Sbjct: 240 ASYHGLVYSDTPFPPFILRARLSLLRDMGSAPSPFNSWLFIQGLEHLNLRIKQHSQSALE 299 Query: 301 IAHYLQNHPKVQAVYYPGLESDKNHANAVKYFDEGMFSGLLSFEVGDFELAQKIADSVKI 360 IA +L+NHPKV+ V YP LE DKN+ NA KY +G SGLLSFEV FE A+KIADSVKI Sbjct: 300 IAKWLKNHPKVKRVNYPLLEGDKNYENAKKYL-KGGASGLLSFEVESFEEAKKIADSVKI 358 Query: 361 FTLATNIGDTKSIITHSASTTHRQVSAEGLKKAGVTPGLVRLSIGLEDYRDLIEDLAQAI 420 F+ NIGD+KSIITH ASTTH+Q+SAE L+ AGV+ GL+RLSIGLE DLI DL QA+ Sbjct: 359 FSRVVNIGDSKSIITHPASTTHQQLSAEELELAGVSEGLIRLSIGLEVVEDLIADLEQAM 418 Query: 421 D 421 + Sbjct: 419 E 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: 538 Number of extensions: 14 Number of successful extensions: 3 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: 419 Length adjustment: 32 Effective length of query: 390 Effective length of database: 387 Effective search space: 150930 Effective search space used: 150930 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