Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate AO353_24330 AO353_24330 cystathionine beta-lyase
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24330 Length = 389 Score = 241 bits (614), Expect = 3e-68 Identities = 154/386 (39%), Positives = 210/386 (54%), Gaps = 19/386 (4%) Query: 3 MQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAI-----GRHKGYEYSRSGNPTRFALEE 57 +QT L H I D G V+ P+Y+ ST GR K Y Y R NP+ AL + Sbjct: 7 VQTLLAHASIEPDQHHGFVNTPVYRGSTVAFPTCESMREGRQK-YTYGRWNNPSTEALTQ 65 Query: 58 LIADLEGGVKGFAFASGLAGIH-AVFSLLQSGDHVLLGDDVYGGTFRLFNQVLVKNGLSC 116 + LEG SGL+ A+ S++ +GDH+L+ D+VY QV + G+ Sbjct: 66 ALQQLEGAEGTVLCPSGLSACTTAILSVVGAGDHLLIADNVYSPIRAFCEQVGQRLGIEV 125 Query: 117 TIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATP 176 T D + + I +KPNTKA+Y E+P + L+I D+ A VA +H +L I DNT+ TP Sbjct: 126 TFYDPTIGAGIVDFLKPNTKAIYTESPGSLTLEIQDIPAIAKVAHEHDILVITDNTWGTP 185 Query: 177 YYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSW 236 Y L LG D+ + TKY+ GHSD V G V+ + A + F +G P D Sbjct: 186 LYFPSLELGVDLSIMAATKYIVGHSDAVLGTVSASKRAW-DSLKRFHFNMGLFASPDDVT 244 Query: 237 LLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGM 296 L RG++TL +R+E H KNA VA++LE +VE VYYP L +HP ++L K+ +G SG+ Sbjct: 245 LALRGMRTLDVRLERHYKNATTVAKWLETREEVEAVYYPALESHPQHQLWKRDFKGASGL 304 Query: 297 LSFTLKNDSEAV--AFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREAAG--IR 352 LSF K ++A A ++SL LF +G S GG ESL I PK R A I Sbjct: 305 LSFVTKPSTQAAADALLDSLSLFSIGYSWGGFESLAMI-------ADPKPVRSATSWEID 357 Query: 353 DGLVRLSVGIEHEQDLLEDLEQAFAK 378 LVRL +G+E DL+EDLEQ FAK Sbjct: 358 GHLVRLHIGLEDPSDLIEDLEQGFAK 383 Lambda K H 0.319 0.137 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: 352 Number of extensions: 15 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: 380 Length of database: 389 Length adjustment: 30 Effective length of query: 350 Effective length of database: 359 Effective search space: 125650 Effective search space used: 125650 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 (21.7 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