Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate H281DRAFT_04486 H281DRAFT_04486 O-acetylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Burk376:H281DRAFT_04486 Length = 465 Score = 249 bits (637), Expect = 9e-71 Identities = 154/416 (37%), Positives = 217/416 (52%), Gaps = 42/416 (10%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPG--------EHQGFEYSRTHNPTRFAYE 70 TLA+H G +PDP+TGA PIY T++++ E G YSR NPT +E Sbjct: 14 TLALHAGAAPDPATGARATPIYQTTSFSFRDSDHAAALFNMERAGHVYSRISNPTVAVFE 73 Query: 71 RCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 VAALE G A ASG AA ++ L+ GSH+VA LYGG+ L RR G+ Sbjct: 74 ERVAALENGAGAIGTASGQAALHLAIVTLMGRGSHIVASSALYGGSHNLLHYTLRRF-GI 132 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189 + +FV D A++AA+R +T++++ ET NP L ++D+A +A IA +H + +VD+TF Sbjct: 133 ETTFVKPGDIDAWRAALRPNTRLLFGETLGNPGLDVLDVATVAQIAHEHRVPLLVDSTFT 192 Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQ---------- 239 +P L +P GAD V HSATK+L GH +GG+ V G + F + Sbjct: 193 TPYLLKPFEHGADFVYHSATKFLGGHGTTIGGVLVDGGTFDFDASGRFPEFTEPYEGFHG 252 Query: 240 ---------------------NSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQW 278 G P ++ L+G++TLPLRM H N + ++ Sbjct: 253 IIFSEESTAAPFLLRARREGLRDFGACLHPQAAWQLLQGIETLPLRMERHVANTRRVVEF 312 Query: 279 LETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKTELFTLA 337 L H A+E V YP L +HP H LAKR + G G + S L+G A + F E LF+ Sbjct: 313 LAGHAAVEAVAYPELPTHPDHALAKRLLPRGAGAVFSFNLRGDRAAGRSFIEALSLFSHL 372 Query: 338 ESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 ++G SLV HPA TH + A GI++ +RLS+G+ED DL DL+R L Sbjct: 373 ANVGDARSLVIHPASTTHFRMDAAALAAAGIAEGTIRLSIGLEDPDDLIDDLKRGL 428 Lambda K H 0.320 0.134 0.391 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: 524 Number of extensions: 30 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: 397 Length of database: 465 Length adjustment: 32 Effective length of query: 365 Effective length of database: 433 Effective search space: 158045 Effective search space used: 158045 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 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