Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Synpcc7942_0370 Synpcc7942_0370 O-acetylhomoserine/O-acetylserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__SynE:Synpcc7942_0370 Length = 434 Score = 242 bits (618), Expect = 1e-68 Identities = 157/426 (36%), Positives = 224/426 (52%), Gaps = 51/426 (11%) Query: 17 LATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQ---------GFEYSRTHNPTRF 67 L TLA+H GQ PDP+TG+ PIY T++Y EH G Y+R NPT Sbjct: 5 LETLALHAGQKPDPTTGSRAVPIYQTTSYVFED-AEHAANLFALKAFGNIYTRLMNPTTD 63 Query: 68 AYERCVAALEGGTRAFAFASGMAATS-TVMELLDAGSHVVAMDDLYGGTFRLFERVRRRT 126 E+ +AAL GGT A A +SG AA + + AG ++++ +LYGGT LF +R Sbjct: 64 VLEQRLAALHGGTGAVATSSGQAAIFYAIAAITSAGQNIISTTNLYGGTINLFRHTLKRF 123 Query: 127 AGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDN 186 G++ FVD +D ++ AAI +T++V+ E+ NP + D AIA IA G+ +VDN Sbjct: 124 -GIEVRFVDSSDASSVAAAIDENTRLVYTESIGNPKGNVDDFEAIAAIAHDSGIPFIVDN 182 Query: 187 TFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV---------------------- 224 T + P L PL GAD+VV S TK GH +GGI + Sbjct: 183 TVSPPPLFNPLEHGADVVVLSLTKLAGGHGTSLGGIVIEKGDFPWNNGKFPEIAGPDPSY 242 Query: 225 --------VGDNAE-LAEQMAF-------LQNSIGGVQGPFDSFLALRGLKTLPLRMRAH 268 G++ E +A +A+ L IG PF++ L G++TLPLR H Sbjct: 243 HGVNFWDAFGNHPEAVAPGLAYVLKIRTGLLRDIGATLSPFNAQQVLLGVETLPLRAERH 302 Query: 269 CENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRF 327 NA A+A+WLE HP + V YPGL SHP + A+R + +G G I+ ++GG +A KRF Sbjct: 303 VRNAQAVAEWLERHPLVTWVNYPGLPSHPDYDRAQRYLPNGAGAILGFGVQGGLEAGKRF 362 Query: 328 CEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRG 387 +L + ++ ++LV HPA TH + + G+S VRLSVG+E L D+ Sbjct: 363 ISAVKLASNLANVLDAKTLVIHPASTTHQQLSPEEQAAAGVSPDFVRLSVGLEHLDDILA 422 Query: 388 DLERAL 393 DL++AL Sbjct: 423 DLDQAL 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: 465 Number of extensions: 24 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: 397 Length of database: 434 Length adjustment: 31 Effective length of query: 366 Effective length of database: 403 Effective search space: 147498 Effective search space used: 147498 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 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