Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate WP_029134797.1 A3GO_RS0119315 cystathionine gamma-synthase
Query= BRENDA::L0EK12 (534 letters) >NCBI__GCF_000428045.1:WP_029134797.1 Length = 390 Score = 281 bits (720), Expect = 2e-80 Identities = 157/366 (42%), Positives = 217/366 (59%), Gaps = 4/366 (1%) Query: 168 TPVVNTSAYFFKKTADLIDFKEKRQTSYEYGRYG-NPTSTVLEEKISELEGAESTVLMAS 226 TP+ T+ + F TA L+D E RQ Y RYG NPT LE K++ LEGAE+ AS Sbjct: 28 TPIYATTTFKFADTAALLDVVEGRQAGSLYTRYGLNPTIQALEAKLASLEGAEAAFAFAS 87 Query: 227 GMCASIVLLMALVPAGGHLVTTTDCYRKTRIFIETVLPKMGITTTVVDPADVGALESALE 286 GM A L + G +V D Y T I LP +GI T ++ +++ L+ L Sbjct: 88 GMAAEAALFLTHGREG--IVCIGDAYGGTLELIAEQLPLLGIPTHLILGSELNRLDGLLA 145 Query: 287 QNNVSLFFTESPTNPFLRCVDIKLVSELCHKHGALLCIDGTFATPLNQKALALGADLIMH 346 V L F E+PTNP L DI +++ H HGALL +D TFA+P+NQ+ LALGAD+++H Sbjct: 146 -GGVRLVFLETPTNPALELFDIAALADQVHAHGALLAVDNTFASPVNQQPLALGADVVVH 204 Query: 347 SCTKYMGGHHDVLGGCISGSDKLISQIRILHHILGGALNPNAAYLFIRGMKTLHLRVQQQ 406 S TKY+GGH D+ G + GS L+ + LG P R ++TL +RV+QQ Sbjct: 205 SATKYLGGHSDLTAGALMGSKALLDPVWGWRKNLGSMPAPETCGQLARSLRTLVVRVRQQ 264 Query: 407 NSTGMRMAKLLEAHPKVKRVYYPGLPSHPEHELAMRQMTGFGGVVSFEIDGDLTTTIKFV 466 N+T +A+ + HP+++RV+YPGL P HELA+RQM+GFGG+++ E+D D T V Sbjct: 265 NATAQAIAEAMAHHPRIRRVFYPGLTDFPGHELAVRQMSGFGGMLTIEVDADTAATSAMV 324 Query: 467 DSLKIPYIAASFGGCESIVDQPAILSYWDLPASERAKYKIYDNLVRFSFGVEDFEDLKAD 526 D LK+ +AAS GG ES+V QP ++ L ERA+ I +VR S G+ED DL AD Sbjct: 325 DRLKLFSLAASLGGVESLVTQPVTTTHHGLSEDERARRGISGAMVRLSVGLEDAGDLIAD 384 Query: 527 ILQALE 532 + QAL+ Sbjct: 385 LQQALD 390 Lambda K H 0.319 0.134 0.393 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: 450 Number of extensions: 20 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: 534 Length of database: 390 Length adjustment: 33 Effective length of query: 501 Effective length of database: 357 Effective search space: 178857 Effective search space used: 178857 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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