Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_004514406.1 GMET_RS04100 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000012925.1:WP_004514406.1 Length = 427 Score = 255 bits (652), Expect = 1e-72 Identities = 159/417 (38%), Positives = 232/417 (55%), Gaps = 41/417 (9%) Query: 17 LATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPG-------EHQGFEYSRTHNPTRFAY 69 + T AI GG +P V+ +T+ ++ E GF Y+R NPT A+ Sbjct: 7 IETQAIQGGYTPKAGDPRVVTICQSTTFKYDNADHVTKLFDLEEPGFFYTRLGNPTTDAF 66 Query: 70 ERCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAG 128 E+ +A +EGG A A ++G AAT+ ++ + AG H V LYGGT+ LF + G Sbjct: 67 EQKLAMMEGGVGALATSAGQAATTLSIFNICQAGQHFVTASTLYGGTYNLFACTLPKM-G 125 Query: 129 LDFSFVDLTDPA-AFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNT 187 ++ SFVD PA AA R +TK ++ ET NP L ++D A + IA++ G+ ++D+T Sbjct: 126 IEVSFVDPEAPADEILAAFRPNTKALFAETIGNPGLNVLDFAKFSAIAQEKGVPLIIDST 185 Query: 188 FASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDN--------AELAE------ 233 FA+P L RP GA++VVHSATKY++G + VGG+ V G N EL E Sbjct: 186 FATPYLCRPFEHGANVVVHSATKYIDGLATSVGGVIVDGGNFDWGNGRFPELTEPDSSYH 245 Query: 234 ---------QMAF-------LQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQ 277 +A+ L IG PF+SFL GL+TLPLRM+ H +NALALAQ Sbjct: 246 GLQYVKTFGNLAYIIKARVQLMRDIGTTPSPFNSFLFTNGLQTLPLRMQRHSDNALALAQ 305 Query: 278 WLETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKTELFTL 336 +LE+HP++ V YPGL+SH H A++ + G G+++ +KGG +A K+F E L L Sbjct: 306 FLESHPSVSWVKYPGLSSHASHDRAQKYLPQGCSGVLTFGIKGGTEAGKKFMEACRLVAL 365 Query: 337 AESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 +G S V HPA TH + ++ G++ L+RLSVGIE + D+ D+++AL Sbjct: 366 VVHVGDARSCVLHPASTTHRQLTAEQQTASGVTPDLIRLSVGIEHIDDIIADVDQAL 422 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: 456 Number of extensions: 25 Number of successful extensions: 5 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: 397 Length of database: 427 Length adjustment: 31 Effective length of query: 366 Effective length of database: 396 Effective search space: 144936 Effective search space used: 144936 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: 50 (23.9 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