Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate RR42_RS31610 RR42_RS31610 cystathionine beta-lyase
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__Cup4G11:RR42_RS31610 Length = 402 Score = 244 bits (622), Expect = 4e-69 Identities = 156/390 (40%), Positives = 216/390 (55%), Gaps = 25/390 (6%) Query: 5 TKLIHGGISEDATT-GAVSVPIYQTSTYR-------QDAIGRHKGYE----YSRSGNPTR 52 T+LIH G G V+VP+ +TST R D RH E Y R G T Sbjct: 7 TQLIHAGTPPFVQGHGPVNVPVVRTSTVRFENSDAYDDIRARHARGERVSSYGRHGMDTH 66 Query: 53 FALEELIADLEGGVKGFAFASGLAGIHAVF-SLLQSGDHVLLGDDVYGGTFRLFNQVLVK 111 ALE+ IA LEGG + F SGLA I F +LL GDH L+ D VY RL +L + Sbjct: 67 RALEDAIAGLEGGNRAFLAPSGLAAISLTFLALLSPGDHALVVDSVYAPVRRLEQTLLRR 126 Query: 112 NGLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDN 171 G+ + S + I+PNT+ LYLE+PS+ L ++ DL + +A HG++ DN Sbjct: 127 LGIEVSYFSPSQ-DDLDALIRPNTRLLYLESPSSLLYEVLDLPRLVQIAHRHGVVVATDN 185 Query: 172 TFATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLG 231 T+A+ + PL LG DI + TKY+ GHSD++ G V +EALA+ IA + G + Sbjct: 186 TWASGHALQPLALGVDISILASTKYISGHSDLMQGAVVVKDEALARRIADAHDGFGLAIS 245 Query: 232 PQDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMR 291 D++L RGI+TL +R+ HQ+NAL VA+FLE H V RV+YP LP+ P + L + Sbjct: 246 ADDAYLALRGIRTLAVRLAQHQRNALAVAQFLEAHEAVGRVFYPALPSDPGHALWLRDFS 305 Query: 292 GFSGMLSFTLKNDSEAVA--FVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQREAA 349 G +G++SF+L A A V+SL LF LG S GG ESLV + A P+ E + Sbjct: 306 GANGLVSFSLPTADVAAARKLVDSLSLFGLGASWGGYESLVQVAA-------PERLAEHS 358 Query: 350 GIR--DGLVRLSVGIEHEQDLLEDLEQAFA 377 R + ++RL +G+E +DL+ DL Q A Sbjct: 359 YWRGAEPVIRLHIGLEAPEDLIADLAQGLA 388 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: 378 Number of extensions: 19 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: 402 Length adjustment: 31 Effective length of query: 349 Effective length of database: 371 Effective search space: 129479 Effective search space used: 129479 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