Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate AZOBR_RS11340 AZOBR_RS11340 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::L7N4M1 (449 letters) >FitnessBrowser__azobra:AZOBR_RS11340 Length = 436 Score = 442 bits (1136), Expect = e-128 Identities = 220/428 (51%), Positives = 294/428 (68%), Gaps = 8/428 (1%) Query: 18 FETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTTDV 77 F+T +HAGQ PDP T ARA+PIY +TSY FDDT HAA+LF LE PG+IY+RI NPT V Sbjct: 9 FDTLSLHAGQRPDPATGARAVPIYQSTSYVFDDTDHAASLFNLERPGHIYSRISNPTVAV 68 Query: 78 VEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKLG 137 +E+R+AAL+GGV A+ +SGQAA T AI+ L AG HIV+S +YGG+ NL Y+L + G Sbjct: 69 LEERLAALDGGVGAVCTASGQAALTLAIMTLMDAGGHIVASSSIYGGSRNLLAYTLPRFG 128 Query: 138 IEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVDNT 197 I +FV +P DLD ++AA+RP T+ F E + NP +++LD P++S +AH G+PL+VD T Sbjct: 129 ITTTFV-NPRDLDGFRAAIRPETRLLFGEVLGNPGLEVLDIPSLSAIAHEAGLPLMVDAT 187 Query: 198 IATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDW-TQGRFPGFTTPDPSY 256 TPYL +PL+ GAD+V+HS TK+L GHG AI GV++DGG FDW G+FP T P Y Sbjct: 188 FVTPYLCKPLSVGADLVMHSCTKWLAGHGVAIGGVVIDGGTFDWEASGKFPTLTEPYAGY 247 Query: 257 HGVVFA-ELGPPAFALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRVA 315 HG+ FA E GP AF ++AR + LRD+G+ SP NAF + QG+ETL LR++ H+ N ++V Sbjct: 248 HGIDFAEEYGPAAFVMRARAEGLRDFGACMSPMNAFQILQGVETLPLRMKGHIHNTRKVL 307 Query: 316 EFL-----AARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNA 370 FL A V V + LP P H +L P G G+++SF + GG EAG+ F+ Sbjct: 308 GFLESEAYAENGSVAWVTHPELPDHPDHRLRAQLLPHGAGSIISFGIKGGREAGRRFIEK 367 Query: 371 LKLHSHVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLE 430 L L SH+AN+GD +SLVIHPASTTHAQL A GV ++RL++G+E DD++ DL Sbjct: 368 LALFSHLANVGDAKSLVIHPASTTHAQLDAEALAAAGVGEDMIRLSIGLEDCDDLIDDLR 427 Query: 431 LGFAAARR 438 AA + Sbjct: 428 QALRAATK 435 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: 583 Number of extensions: 21 Number of successful extensions: 5 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: 436 Length adjustment: 32 Effective length of query: 417 Effective length of database: 404 Effective search space: 168468 Effective search space used: 168468 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