Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate BWI76_RS24285 BWI76_RS24285 cystathionine beta-lyase
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__Koxy:BWI76_RS24285 Length = 395 Score = 186 bits (472), Expect = 1e-51 Identities = 122/396 (30%), Positives = 207/396 (52%), Gaps = 26/396 (6%) Query: 3 MQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAI--------GRHKG-YEYSRSGNPTRF 53 + T L+H G S+ T G+V+ I + S+ D + R KG Y R G T F Sbjct: 6 LDTALVHAGRSKKYTQGSVNSVIQRASSLVFDTVEAKKHATRNRAKGELFYGRRGTLTHF 65 Query: 54 ALEELIADLEGGVKGFAFASGLAGI-HAVFSLLQSGDHVLLGDDVYGGTFRLFNQVLVKN 112 +L+E + +LEGG F G A + + + + ++ GDH+L+ + Y T ++L K Sbjct: 66 SLQEAMCELEGGAGCALFPCGAAAVANTILAFVEQGDHILVTNTAYEPTQDFCTKILAKL 125 Query: 113 GLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHG--LLTIVD 170 G++ D I + ++PNT+ ++LE+P + +++ D+ + + + ++D Sbjct: 126 GVTTGWFDPLIGGDIARLVQPNTRVVFLESPGSITMEVHDVPAIVAAVRRVAPEAIIMID 185 Query: 171 NTFATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNA--IGG 228 NT+A L G DI +GTKYL GHSD + G +N AQ +NA +G Sbjct: 186 NTWAAGVLFKALEFGIDISIQAGTKYLIGHSDAMVGTAVSNERCWAQ---LRENAYLMGQ 242 Query: 229 VLGPQDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKK 288 ++ +++ RG++TL +R+ H +++L +AE+L +HP+V RV +P LP +E ++ Sbjct: 243 MVDADTAYMTSRGLRTLAVRLRQHHESSLQIAEWLAQHPQVARVNHPALPGSKGHEFWQR 302 Query: 289 QMRGFSGMLSFTLK---NDSEAVAFVESLKLFILGESLGGVESLV--GIPAFMTHACIPK 343 G SG+ SF L D+E A+++ LF + S GG ESL+ P + A P Sbjct: 303 DFTGSSGLFSFVLNKRLTDAELSAYLDHFSLFSMAYSWGGFESLILANQPEHIA-AIRPD 361 Query: 344 TQREAAGIRDGLVRLSVGIEHEQDLLEDLEQAFAKI 379 + + +G L+RL +G+E+ DL +DL FA+I Sbjct: 362 AEVDFSGT---LIRLHIGLENVTDLQDDLAAGFARI 394 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: 316 Number of extensions: 21 Number of successful extensions: 7 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: 395 Length adjustment: 30 Effective length of query: 350 Effective length of database: 365 Effective search space: 127750 Effective search space used: 127750 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