Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_007053689.1 BL_RS04385 cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000007525.1:WP_007053689.1 Length = 394 Score = 358 bits (919), Expect = e-103 Identities = 197/383 (51%), Positives = 265/383 (69%), Gaps = 11/383 (2%) Query: 17 LATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSP-GEHQGFEYSRTHNPTRFAYERCVAA 75 +AT AIH GQ PDP+TGAV+ PI+ATST+ Q G G +YSR+ NPTR +++ +AA Sbjct: 14 IATRAIHAGQEPDPTTGAVVTPIFATSTFKQDGVLGLRGGHDYSRSINPTRTSFDEQLAA 73 Query: 76 LEGGTRAFAFASGMAATSTVME-LLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFV 134 +EGG A +F+SG+AA ++ + G +++ +D+YGGT+RL +V G+ V Sbjct: 74 VEGGKYALSFSSGLAAIDVLLRSTIKPGDNILLGNDVYGGTYRLLSKVFVPW-GVGLDVV 132 Query: 135 DLTDPAAFKAAIRADT-KMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPML 193 ++TD A + A+ + + VW+ETP+NP+L + DIAA +A K+G VDNTFASP L Sbjct: 133 NITDLKAVETALASKHYQYVWVETPSNPLLNITDIAATTEVAHKYGTKVAVDNTFASPAL 192 Query: 194 QRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFL 253 Q PL+ GAD+VV+S TKY+ GHSD+VGG VV D E E++AFLQN+ G V PFDS+L Sbjct: 193 QHPLADGADVVVYSTTKYIGGHSDVVGGAVVVNDE-ETREKVAFLQNAAGAVPSPFDSWL 251 Query: 254 ALRGLKTLPLRMRAHCENALALAQWLETHPA--IEKVIYPGLASHPQHVLAKRQM-SGFG 310 +RGLKTL LR++ H NAL +A+WLE+ P+ IE+V YPGL SHP H +A RQM GFG Sbjct: 252 DIRGLKTLDLRVKRHSANALKVAEWLESQPSDVIERVWYPGLESHPGHEIAARQMHGGFG 311 Query: 311 GIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISD 370 GIVS+ L G +AAK F + T++FTLAESLGGVESL+ PA MTHAS+ L + Sbjct: 312 GIVSVQLAAGAEAAKHFVDHTQIFTLAESLGGVESLIEVPAAMTHASV---AGTTLQVPA 368 Query: 371 ALVRLSVGIEDLGDLRGDLERAL 393 LVR+SVGIE+ DL DL++AL Sbjct: 369 NLVRISVGIENADDLIADLKQAL 391 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: 509 Number of extensions: 25 Number of successful extensions: 8 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: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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 12 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