Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate RR42_RS31610 RR42_RS31610 cystathionine beta-lyase
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__Cup4G11:RR42_RS31610 Length = 402 Score = 245 bits (625), Expect = 2e-69 Identities = 156/393 (39%), Positives = 218/393 (55%), Gaps = 25/393 (6%) Query: 2 HMQTKLIHGGISEDATT-GAVSVPIYQTSTYR-------QDAIGHHKGYE----YSRSGN 49 H T+LIH G G V+VP+ +TST R D H E Y R G Sbjct: 4 HRDTQLIHAGTPPFVQGHGPVNVPVVRTSTVRFENSDAYDDIRARHARGERVSSYGRHGM 63 Query: 50 PTRFALEELIADLEGGVKGFAFASGLAGIHAVF-SLLQSGDHVLLGDDVYGGTFRLFNKV 108 T ALE+ IA LEGG + F SGLA I F +LL GDH L+ D VY RL + Sbjct: 64 DTHRALEDAIAGLEGGNRAFLAPSGLAAISLTFLALLSPGDHALVVDSVYAPVRRLEQTL 123 Query: 109 LVKNGLSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTI 168 L + G+ + S + I+PNT+ LYLE+PS+ L ++ DL + +A HG++ Sbjct: 124 LRRLGIEVSYFSPSQ-DDLDALIRPNTRLLYLESPSSLLYEVLDLPRLVQIAHRHGVVVA 182 Query: 169 VDNTFATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGG 228 DNT+A+ + PL LG DI + + TKY+ GHSD++ G V +EALA+ IA + G Sbjct: 183 TDNTWASGHALQPLALGVDISILASTKYISGHSDLMQGAVVVKDEALARRIADAHDGFGL 242 Query: 229 VLGPQDSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKK 288 + D++L RGI+TL +R+ HQ+NAL VA+FLE H V RV+YP LP+ P + L + Sbjct: 243 AISADDAYLALRGIRTLAVRLAQHQRNALAVAQFLEAHEAVGRVFYPALPSDPGHALWLR 302 Query: 289 QMRGFSGMLSFTL--KNDSEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQR 346 G +G++SF+L + + A V+SL LF LG S GG ESLV V A P+ Sbjct: 303 DFSGANGLVSFSLPTADVAAARKLVDSLSLFGLGASWGGYESLVQVAA-------PERLA 355 Query: 347 EAAGIR--DGLVRLSVGIEHEQDLLEDLEQAFA 377 E + R + ++RL +G+E +DL+ DL Q A Sbjct: 356 EHSYWRGAEPVIRLHIGLEAPEDLIADLAQGLA 388 Lambda K H 0.318 0.136 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: 383 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: 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 ( 7.3 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