Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_011840796.1 RSPH17029_RS05580 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::L7N4M1 (449 letters) >NCBI__GCF_000015985.1:WP_011840796.1 Length = 430 Score = 414 bits (1065), Expect = e-120 Identities = 217/421 (51%), Positives = 281/421 (66%), Gaps = 3/421 (0%) Query: 18 FETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTTDV 77 F+T QIHAG PDP T AR +PIY TT+Y F D HAA LF LE G IY+R+ NPT Sbjct: 9 FDTLQIHAGAKPDPATGARQVPIYQTTAYVFRDAEHAARLFNLEEVGYIYSRLTNPTVMA 68 Query: 78 VEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKLG 137 + +R+AALEGG A+ SSG AA+ A+ L G +IV+S RLYGGT F ++ + G Sbjct: 69 LAERVAALEGGAGAVCCSSGHAAQIMALFPLMAPGRNIVASTRLYGGTITQFSQTIRRFG 128 Query: 138 IEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVDNT 197 FVD DD +AA+ +T+A F ETI+NP + D AVS +A + G+PLIVDNT Sbjct: 129 WSAKFVDF-DDPAAIEAAIDSDTRALFCETIANPGGVITDLDAVSAIADKMGLPLIVDNT 187 Query: 198 IATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDWTQG-RFPGFTTPDPSY 256 ATP+L +P+ GA +VVHSATKYL G+G GVIVD G FDW+ +FP + P+P+Y Sbjct: 188 TATPWLCRPIEHGATLVVHSATKYLTGNGTVTGGVIVDSGKFDWSASDKFPSLSQPEPAY 247 Query: 257 HGVVFAE-LGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRVA 315 HG+VF + LGP A+ + LRD G +P A G+ETLSLR+ RHV NAQ+VA Sbjct: 248 HGLVFHKALGPMAYTFHSIAVGLRDLGMTMNPQGAHYTLMGIETLSLRMARHVENAQKVA 307 Query: 316 EFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALKLHS 375 +L V V+YAGLPSSPWH R R+ PKG GA+ +F + GG +A A V+AL+L S Sbjct: 308 AWLEQDPRVEFVSYAGLPSSPWHGRVARICPKGAGALFTFAVKGGYDACVALVDALQLFS 367 Query: 376 HVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLELGFAA 435 HVAN+GD RSLVIH ASTTH QL+P +Q+A G +P +VR+++GIE DD++ADL+ A Sbjct: 368 HVANLGDTRSLVIHSASTTHRQLTPEQQVAAGAAPNVVRISIGIEDADDLIADLDQALAK 427 Query: 436 A 436 A Sbjct: 428 A 428 Lambda K H 0.318 0.134 0.394 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: 586 Number of extensions: 23 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: 449 Length of database: 430 Length adjustment: 32 Effective length of query: 417 Effective length of database: 398 Effective search space: 165966 Effective search space used: 165966 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: 51 (24.3 bits)
This GapMind analysis is from Aug 31 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