Align cystathionine gamma-lyase; EC 4.4.1.1 (characterized)
to candidate WP_012566511.1 RC1_RS06305 O-acetylhomoserine aminocarboxypropyltransferase
Query= CharProtDB::CH_122519 (419 letters) >NCBI__GCF_000016185.1:WP_012566511.1 Length = 437 Score = 202 bits (515), Expect = 1e-56 Identities = 143/430 (33%), Positives = 210/430 (48%), Gaps = 42/430 (9%) Query: 27 FATLAVHAGAPHDPTTGAVIAPISLSTTFAQESVGKPVGLYE-------YTRSSNPNRDN 79 F T A+HAGA DPTTGA PI +T++ + V L+ Y+R +NP Sbjct: 9 FETRAIHAGAAPDPTTGARATPIYQTTSYVFDDVEDAAALFNLEKVGFIYSRLTNPTVSV 68 Query: 80 FEEAVASLEHAKYALAFSSGSATTATILHSL-APGSHVVSVSDVYGGT-HRYFTKVAAAH 137 E +A LE A SSG A L L PG +V+ +YGGT +++ A Sbjct: 69 LEARLADLEGGAGATCTSSGHAAQLLALFPLLTPGDEIVASRQLYGGTLNQFANSFPRAF 128 Query: 138 GVNVSFSSCLELDVEKLIRPNETKLVWIETPSNPTLALVDIRKVAAVAHRHGVLVVVDNT 197 G F + + + +TK ++IE+ +NP ++DI +A +A G+ ++VDNT Sbjct: 129 GWKTVFVDSDDPENFRRALTPKTKAIFIESLANPGGVVLDIEAIARIADGAGIPLIVDNT 188 Query: 198 FMSPYVQNPLDHGADVVIHSVTKYINGHSDVLMGVA------------------------ 233 +PY+ PLDHGA +V+HS TK++ GH + + GV Sbjct: 189 LATPYLCRPLDHGATLVVHSTTKFLGGHGNSVGGVVIDSGRFDWSKDGRFPALSEPEPGY 248 Query: 234 ---AFNSDELKERFTFLQNAI-----GAVPSPFDCWLAHRGLKTLHLRAREATANATAVA 285 F++ FT +AI G +P + +L G++TL LR +ANA AVA Sbjct: 249 HGMRFHATFGALAFTIHGHAIGLRDLGPSQAPLNAFLTLTGIETLALRMERHSANALAVA 308 Query: 286 LALESSPHVISVNYPGLNSHPNREIAVKQHRKGMGGGMLSFRIKGGHKAAHLFCEYTKIF 345 L+ P V VNY GL +A K +G G + +F +KGG++A E K+F Sbjct: 309 QHLKQHPAVAWVNYAGLPDSRYHALARKYLPRG-AGSVFTFGLKGGYEAGVKLVESVKLF 367 Query: 346 TLAESLGGVESLCEVPSSMTHAGIPKEEREAAGVYDDLVRMSCGIEDVEDLTADTMQALE 405 + ++G SL P+S TH+ + E AAG D+VR+S GIE VED+ AD QAL Sbjct: 368 SHLANIGDTRSLIIHPASTTHSQLSPEGLAAAGAGPDVVRLSVGIESVEDIIADLDQALA 427 Query: 406 RAVAASQALE 415 A ++A E Sbjct: 428 TATGTARAAE 437 Lambda K H 0.316 0.130 0.377 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: 496 Number of extensions: 25 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 419 Length of database: 437 Length adjustment: 32 Effective length of query: 387 Effective length of database: 405 Effective search space: 156735 Effective search space used: 156735 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