Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate WP_085773091.1 B1812_RS19675 cystathionine beta-lyase
Query= BRENDA::L0EK12 (534 letters) >NCBI__GCF_002117405.1:WP_085773091.1 Length = 398 Score = 198 bits (504), Expect = 3e-55 Identities = 127/369 (34%), Positives = 190/369 (51%), Gaps = 13/369 (3%) Query: 166 ITTPVVNTSAYFFKKTADLIDFKEKRQTSYEYGRYGNPTSTVLEEKISELEGAESTVLMA 225 + TPV S F D E+ + Y Y G PT+ LEE SEL GA +TVL Sbjct: 32 VNTPVYRGSTVLFPTAEDF----ERHRQPYTYATKGTPTTRGLEEAWSELSGATTTVLAP 87 Query: 226 SGMCASIVLLMALVPAGGHLVTTTDCYRKTRIFIETVLPKMGITTTVVDPADVGALESAL 285 SG+ A + LM AG HL+ T Y TRIF + VL + G+ T DP +GA AL Sbjct: 88 SGLAAIALALMTATKAGDHLLVTDSAYGPTRIFCDGVLKRFGVETQYYDPR-LGAGVGAL 146 Query: 286 EQNNVSLFFTESPTNPFLRCVDIKLVSELCHKHGALLCIDGTFATPLNQKALALGADLIM 345 + N S ESP + + D+ ++ GA + +D T+ATPL G D+ + Sbjct: 147 MRENTSAILAESPGSLTMEVQDVPAIAAAAAARGACVILDNTWATPLFFPPFERGVDINV 206 Query: 346 HSCTKYMGGHHDVLGGCISGSDKLISQIRILHHILGGALNPNAAYLFIRGMKTLHLRVQQ 405 + TKY+ GH D+L G +S + K +++R + A+L +RG++T+ LR+++ Sbjct: 207 EAGTKYLSGHADLLLGLVSANAKWATRLRNSFDAFAMVPGGDDAFLALRGLRTMELRLRE 266 Query: 406 QNSTGMRMAKLLEAHPKVKRVYYPGLPSHPEHELAMRQMTGFGGVVSFEIDGDLTTTI-K 464 Q G+ +A+ LE +V R+ +P LP+HP+H L R +G GV S ++ + Sbjct: 267 QQRAGLEIAQWLEGRSEVLRLLHPALPAHPDHALWKRDFSGAAGVFSVVLNPAPKPCVDA 326 Query: 465 FVDSLKIPYIAASFGGCESIVDQPAILSYWDLPASERAK-YKIYDNLVRFSFGVEDFEDL 523 F+++L + I S+GG ES+V +D S A + +RFS G+ED EDL Sbjct: 327 FLNALTLFGIGYSWGGYESLVIP------FDCARSRTATCFAPEGPCLRFSIGLEDVEDL 380 Query: 524 KADILQALE 532 KAD+ A E Sbjct: 381 KADLAAAFE 389 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: 455 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: 398 Length adjustment: 33 Effective length of query: 501 Effective length of database: 365 Effective search space: 182865 Effective search space used: 182865 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