Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate 3607379 Dshi_0793 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)
Query= BRENDA::L7N4M1 (449 letters) >FitnessBrowser__Dino:3607379 Length = 431 Score = 415 bits (1066), Expect = e-120 Identities = 214/429 (49%), Positives = 283/429 (65%), Gaps = 3/429 (0%) Query: 10 ADPTAHWSFETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTR 69 +D T + F+T QIHAG PDP T AR PIY TT Y F D HAAALF L+ G IY+R Sbjct: 2 SDDTPSYGFDTLQIHAGARPDPATGARQTPIYQTTGYVFRDADHAAALFNLQEVGYIYSR 61 Query: 70 IGNPTTDVVEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLF 129 + NPT V+++RIA LEGGV A+ SSG AA+ A+ L G +IV S RLYGGT F Sbjct: 62 LTNPTVAVLQERIATLEGGVGAVCCSSGHAAQIMALFPLMQPGCNIVVSTRLYGGTVTQF 121 Query: 130 HYSLAKLGIEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNG 189 ++ + G FVD DDLD +AA+ +T+A F E I+NP ++D A++++A G Sbjct: 122 GQTIKRFGWSAKFVDF-DDLDAVRAAIDDDTRAVFGEAIANPGGYIMDVRAIADIADAAG 180 Query: 190 VPLIVDNTIATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDWT-QGRFPG 248 +PLI+DNT ATPYL +P+ GA +VVHS TKYL G+G G +VD G FDW G+FP Sbjct: 181 IPLIIDNTTATPYLCRPIEHGATLVVHSTTKYLTGNGTVTGGCVVDSGKFDWAASGKFPS 240 Query: 249 FTTPDPSYHGVVFAE-LGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERH 307 + P+P+YHG+ FAE GP AF LRD G +P A G+ETLSLR+ RH Sbjct: 241 LSEPEPAYHGLRFAETFGPLAFTFHGIAVGLRDLGMTMNPQGAHYTLMGIETLSLRMARH 300 Query: 308 VANAQRVAEFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAF 367 V NA+++A++L A D V V YAGLPSSP+ ER K + P+G GA+ +F + GG EA Sbjct: 301 VENAEKIAKWLEADDRVEFVTYAGLPSSPYFERVKTVCPRGAGALFTFAVKGGYEACIKL 360 Query: 368 VNALKLHSHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILA 427 V++L++ SHVAN+GD RSL+IH ASTTH QL+P +Q A G +P +VRL++GIE DD++A Sbjct: 361 VDSLEIFSHVANLGDTRSLIIHSASTTHRQLTPEQQEAAGAAPNVVRLSIGIEDADDLIA 420 Query: 428 DLELGFAAA 436 DL+ + A Sbjct: 421 DLDQALSKA 429 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: 574 Number of extensions: 27 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: 431 Length adjustment: 32 Effective length of query: 417 Effective length of database: 399 Effective search space: 166383 Effective search space used: 166383 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 Apr 09 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