Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate 351451 BT1923 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)
Query= BRENDA::L7N4M1 (449 letters) >FitnessBrowser__Btheta:351451 Length = 426 Score = 394 bits (1011), Expect = e-114 Identities = 204/415 (49%), Positives = 271/415 (65%), Gaps = 4/415 (0%) Query: 19 ETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTTDVV 78 ET + AG P R LPIY +T++ +D + A LF LE G YTR+ NPT D V Sbjct: 8 ETLCVQAGWTPKKG-EPRVLPIYQSTTFKYDTSEQMARLFDLEDSGYFYTRLQNPTNDAV 66 Query: 79 EQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKLGI 138 +IAALEGGVAA+ SSGQAA +AI N+ AGDH V S +YGGT+NLF ++ KLGI Sbjct: 67 AAKIAALEGGVAAMLTSSGQAANFYAIFNICQAGDHFVCSSAIYGGTFNLFGVTMKKLGI 126 Query: 139 EVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVDNTI 198 +V+FV+ + AA +PNTKA F ETISNP +++LD + +AH +GVPLIVDNT Sbjct: 127 DVTFVNPDASEEEISAAFQPNTKALFGETISNPSLEVLDIEKFARIAHSHGVPLIVDNTF 186 Query: 199 ATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDWT--QGRFPGFTTPDPSY 256 TP +P GADI+VHS TKY+ GH ++ G IVD GNFDW +FPG TPD SY Sbjct: 187 PTPINCRPFEWGADIIVHSTTKYMDGHATSVGGCIVDSGNFDWDAHADKFPGLCTPDESY 246 Query: 257 HGVVFAE-LGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRVA 315 HG+ + + G A+ KA QL+RD GS SP N+FL+ GLETL LR+ +H NAQ+VA Sbjct: 247 HGLTYTKAFGKGAYITKATAQLMRDLGSIQSPQNSFLLNLGLETLHLRMPQHCRNAQKVA 306 Query: 316 EFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALKLHS 375 E+L+ + V VNY GLP + ++ A++ P G+ V+SF L GG + F+++L+ + Sbjct: 307 EYLSKNEKVAWVNYCGLPDNKYYALAQKYMPNGSCGVISFGLKGGRDVSIKFMDSLEFIA 366 Query: 376 HVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLE 430 V ++ D RS V+HPAS TH QLS + + GV P L+RL+VGIE DDI+AD+E Sbjct: 367 IVTHVADARSCVLHPASHTHRQLSDEQLMEAGVRPDLIRLSVGIENADDIIADIE 421 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: 503 Number of extensions: 13 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: 449 Length of database: 426 Length adjustment: 32 Effective length of query: 417 Effective length of database: 394 Effective search space: 164298 Effective search space used: 164298 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 03 2021. The underlying query database was built on Aug 03 2021.
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