Align Cystathionine gamma-lyase; CGL; CSE; Cysteine desulfhydrase; Cysteine-protein sulfhydrase; Gamma-cystathionase; Homocysteine desulfhydrase; EC 4.4.1.1; EC 4.4.1.2 (characterized)
to candidate NP_661504.1 CT0604 O-acetylhomoserine (thiol)-lyase
Query= SwissProt::Q55DV9 (387 letters) >NCBI__GCF_000006985.1:NP_661504.1 Length = 429 Score = 221 bits (563), Expect = 3e-62 Identities = 136/426 (31%), Positives = 218/426 (51%), Gaps = 41/426 (9%) Query: 1 MTQPNNYKIGTNVIHAGQSADKNTGAVIVPISLSTTFLQPSP-------GVLHSEYDYSR 53 M++ N ++ T +HAGQ D TG+ VPI +T+++ + + + Y+R Sbjct: 1 MSEDNTFRFETLQVHAGQEPDPVTGSRAVPIYQTTSYVFENAEHGADLFALRKAGNIYTR 60 Query: 54 SGNPTRKAFEECIAACENAKYALSFASG-LATLTTITHLLKSGDEVISIDDVYGGTRRYF 112 NPT E+ +AA E K AL ASG A I + ++GD ++S +YGGT F Sbjct: 61 LMNPTTDVLEKRMAALEGGKAALGVASGHSAQFIAIATICQAGDNIVSSSYLYGGTYNQF 120 Query: 113 TRVAANFDLKFSFVDLSTLDDLKNAFTDKTRLVWIETPTNPLLKVADIKAVADYVHSRGA 172 ++ FVD + + + A + T+ +++E+ NP V D A+A G Sbjct: 121 KVAFKRLGIEVRFVDGNDQEAFRKAIDENTKALYMESIGNPAFHVPDFDAIAKIARENGI 180 Query: 173 TLVVDNTF-MSPYFQNPLDLGADIVMHSVTKYINGHSDCVMGVLA--------------- 216 L+VDNTF + Y P+D GA IV+ S TK+I GH + G++ Sbjct: 181 PLIVDNTFGCAGYLCRPIDHGASIVVESATKWIGGHGTSMGGIIVDAGTFDWGNGKFPLF 240 Query: 217 TNNDELYAKLKFLQ----------------NSIGAVPSPFDCFLALRGLKTLHVRMEAHQ 260 T E Y LKF + G SPF+ F+ L+GL+TL +R++ H Sbjct: 241 TEPSEGYHGLKFYEAVGELAFIIRARVEGLRDFGPAISPFNSFMLLQGLETLSLRVQRHL 300 Query: 261 KNAFAICNFLEKHPKVERVIYPGLPSHPQHEICKRQMK-GYGGMVVFFVKGSIDQSRSFL 319 N + +LE+H V V YPGL SHP H + K+ + G+G ++ F VKG + + F+ Sbjct: 301 DNTLELARWLERHDAVAWVNYPGLESHPTHALAKKYLTHGFGCVLTFGVKGGYENAVKFI 360 Query: 320 ENIKLFALAESLGGVESLIELPSVMTHASVPAEERAKLGISDTLIRLSVGIEDINDLLAD 379 +++KL + ++G ++L+ P+ TH + AEE+ G++ ++R+SVGIE I+D+ AD Sbjct: 361 DSVKLASHLANVGDAKTLVIHPASTTHQQLSAEEQVSAGVTADMVRVSVGIEHIDDIKAD 420 Query: 380 ISQALD 385 SQA + Sbjct: 421 FSQAFE 426 Lambda K H 0.320 0.135 0.394 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: 430 Number of extensions: 21 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: 387 Length of database: 429 Length adjustment: 31 Effective length of query: 356 Effective length of database: 398 Effective search space: 141688 Effective search space used: 141688 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