Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_012102205.1 CKL_RS08890 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000016505.1:WP_012102205.1 Length = 409 Score = 345 bits (886), Expect = 1e-99 Identities = 196/429 (45%), Positives = 267/429 (62%), Gaps = 21/429 (4%) Query: 14 KPETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTD 73 K T +HG + D T + VPLY + +Y +F +E G YTR+ NPT Sbjct: 2 KFNTKLIHGNLKTDATGATN-VPLYLSNAYAHTSAKKLENIFKGKEMGYSYTRISNPTVT 60 Query: 74 VLEKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKL 133 E+R+A++E G+ A + ASG SA ++++NIVE G EI+ASSSLYGGTY L+ L Sbjct: 61 SFERRIASIENGLIATSAASGMSAIYISIMNIVEPGDEIIASSSLYGGTYTLIR-NLKLL 119 Query: 134 GIKVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNT 193 GIKV F++ D ++A N T+ +AET+GNPKLD LDI +VSK+ KE + L+ID+T Sbjct: 120 GIKVRFLENIDKATLKEAINKNTKLVFAETIGNPKLDVLDIDSVSKICKENNIVLMIDST 179 Query: 194 MPSPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGKFKNFTEPDPSYH 253 + +PYLV PL++GADIV+HS +K++ G SIGGII+DGGS + + K++NF Sbjct: 180 ITTPYLVKPLEYGADIVIHSTSKYINGTSNSIGGIIVDGGSNKYMDLKYENFR------- 232 Query: 254 GLKFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHS 313 + + +GK +AF K + RD+GPA+SPFNA+ L G+ETL LRM+ H Sbjct: 233 --PYTKKYGK--------MAFTAKLKDTIERDIGPALSPFNAFLNLTGIETLSLRMKEHC 282 Query: 314 GNALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKF 373 NAL VAE L ++ KI VNYPGL K Y KKY+ G G I+ F + G EKA KF Sbjct: 283 KNALTVAEHLMQNSKITDVNYPGLENSKYYDLIKKYYSNG-SGGILTFRL-GSKEKAFKF 340 Query: 374 IDGLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILV 433 +D L+L L NIGD KS+ IHP+ST T E+ GV +RLSVG+E+++DIL Sbjct: 341 LDNLKLILNLTNIGDTKSIIIHPSSTICANNTDEEKQQMGVYDDLLRLSVGIEDVEDILE 400 Query: 434 DLEEALKNI 442 D+E ALK I Sbjct: 401 DIENALKYI 409 Lambda K H 0.317 0.137 0.402 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: 447 Number of extensions: 14 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: 442 Length of database: 409 Length adjustment: 32 Effective length of query: 410 Effective length of database: 377 Effective search space: 154570 Effective search space used: 154570 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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