Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate BPHYT_RS13720 BPHYT_RS13720 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::L7N4M1 (449 letters) >FitnessBrowser__BFirm:BPHYT_RS13720 Length = 450 Score = 461 bits (1186), Expect = e-134 Identities = 234/426 (54%), Positives = 302/426 (70%), Gaps = 3/426 (0%) Query: 18 FETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTTDV 77 F+T +HAG PDPTT ARA PIY TTS++F D+ HAAALF +E G++Y+RI NPT V Sbjct: 6 FDTLALHAGAAPDPTTGARATPIYQTTSFSFRDSDHAAALFNMERAGHVYSRISNPTVAV 65 Query: 78 VEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKLG 137 E+R+AALE G A+ +SGQAA AI L GAG HIV+S LYGG++NL HY+L + G Sbjct: 66 FEERVAALENGAGAIGTASGQAALHLAIATLMGAGSHIVASSALYGGSHNLLHYTLRRFG 125 Query: 138 IEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVDNT 197 IE +FV P DLD W+AA+RPNT+ F ET+ NP +D+LD AV+++AH + VPL+VD+T Sbjct: 126 IETTFVK-PGDLDAWRAALRPNTRLLFGETLGNPGLDVLDIAAVAQIAHEHRVPLLVDST 184 Query: 198 IATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDW-TQGRFPGFTTPDPSY 256 TPYL++P GAD V HSATK+LGGHG I GV+VDGG FD+ GRFP FT P + Sbjct: 185 FTTPYLLKPFEHGADFVYHSATKFLGGHGTTIGGVLVDGGTFDFEASGRFPEFTEPYDGF 244 Query: 257 HGVVFAELGPPA-FALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRVA 315 HG+VF+E A F L+AR + LRD+G+ P A+ + QG+ETL LR+ERHVAN +RV Sbjct: 245 HGMVFSEESTVAPFLLRARREGLRDFGACLHPQAAWQLLQGIETLPLRMERHVANTRRVV 304 Query: 316 EFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALKLHS 375 EFLAA V SV Y LP+ P H AKRL P+G GAV SF L G AG++F+ AL L S Sbjct: 305 EFLAAHAAVESVAYPELPTHPDHALAKRLLPRGAGAVFSFNLRGDRAAGRSFIEALSLFS 364 Query: 376 HVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLELGFAA 435 H+AN+GD RSLVIHPASTTH ++ A A G++ G +RL++G+E DD++ DL+ A Sbjct: 365 HLANVGDARSLVIHPASTTHFRMDAAALAAAGIAEGTIRLSIGLEDPDDLIDDLKRALKA 424 Query: 436 ARRFSA 441 A++ SA Sbjct: 425 AQKASA 430 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: 623 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: 450 Length adjustment: 33 Effective length of query: 416 Effective length of database: 417 Effective search space: 173472 Effective search space used: 173472 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