Align cystathionine gamma-lyase (subunit 1/2) (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate AZOBR_RS07765 AZOBR_RS07765 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::B3TNN9 (394 letters) >FitnessBrowser__azobra:AZOBR_RS07765 Length = 429 Score = 203 bits (516), Expect = 9e-57 Identities = 141/419 (33%), Positives = 219/419 (52%), Gaps = 51/419 (12%) Query: 3 FDTKLIHGGISEDKYTGATSVPIYM------------ASTFHQQKIGENEYEYSRSGNPT 50 F+T+ IH G + D TGA PIY AS F+ QK+G + YSR NPT Sbjct: 9 FETRAIHAGAAPDPATGARQTPIYQTTSFVFDDVDDAASLFNLQKVG---FIYSRLTNPT 65 Query: 51 REAVEKLIADLEDGTAGFAFASGSAA-IDTVFSLFSAGDHFVIGNDVYGGTFRLIDAVLK 109 +E+ +A+LE G A +SG AA + +F L GD V +YGGT + Sbjct: 66 VSVLEERLANLEGGAGATATSSGHAAQLLALFPLMEPGDEIVASRKLYGGTLNQLGTSFP 125 Query: 110 R-FGMTFTVVDTRDLQAVKAAITPATKAIYLETPTNPLLRVTDIAAVAKIAKDRGILSII 168 R FG VDT + V+AAIT TKAI++E+ NP VTD+ A+AKIA + GI I+ Sbjct: 126 RAFGWKSVFVDTDQPENVRAAITAKTKAIFVESLANPGGVVTDLEAIAKIADEAGIPLIV 185 Query: 169 DNTFSSPYVQRPLDLGVDIVLHSASKYLGGHSDLVAGLVVT----------KDQALG--- 215 DNT ++PY+ P+ G +V+HS +K+L G+ V G+V+ K AL Sbjct: 186 DNTLATPYLINPIQWGATLVVHSTTKFLSGNGTSVGGVVIDSGSFDWGKSGKFPALSEPD 245 Query: 216 ---------EKIGYLQNAI----------GGILAPQESWLLQRGMKTLSLRMRAHLANAE 256 E G+L I G AP ++L G++TL LRM+ H +A Sbjct: 246 AGYHGLKFQETFGHLAFTIHGHAVGLRDLGPSQAPLNAFLTLNGIETLPLRMQRHSDSAL 305 Query: 257 AIFNYLKNQPLVSKIYYPGDPNNPDYEVAQKQM-HGFGAMISFELQAGLDP-KQFVEQLQ 314 + +L++ P V + Y G ++ +A+K + G GA+++F ++ G D + VE +Q Sbjct: 306 KVAQFLESHPAVGWVSYAGLESSKYNALAKKYLPKGAGAVLTFGVKGGFDTGVKVVENVQ 365 Query: 315 VITLAESLGALESLIEIPALMTHGSIPHDIRLKNGIKDELIRLSVGVEDQKDLLADLER 373 +++ ++G SLI P+ TH + + + + G +++RLS+G+E +D++ADL+R Sbjct: 366 LLSHLANIGDSRSLIIHPSSTTHRQLSPEGQAQAGAGPDVLRLSIGLESVEDIIADLDR 424 Lambda K H 0.318 0.135 0.381 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: 416 Number of extensions: 20 Number of successful extensions: 6 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: 394 Length of database: 429 Length adjustment: 31 Effective length of query: 363 Effective length of database: 398 Effective search space: 144474 Effective search space used: 144474 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: 50 (23.9 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