Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate AO356_24030 AO356_24030 sulfurtransferase
Query= curated2:Q1M0P5 (380 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24030 Length = 921 Score = 226 bits (577), Expect = 2e-63 Identities = 142/390 (36%), Positives = 213/390 (54%), Gaps = 22/390 (5%) Query: 3 MQTKLIHGG-ISEDATTGAVSVPIYQTSTYRQDAIGHHKG----------YEYSRSGNPT 51 ++T L+HG ++ V+VP+ + ST D + + Y GNPT Sbjct: 532 LRTHLVHGARTAKGVGARPVNVPVSRLSTVLFDNLAQMRDARARRDSERVLSYGARGNPT 591 Query: 52 RFALEELIADLEGGVKGFAFASGLAGIHAVF-SLLQSGDHVLLGDDVYGGTFRLFNKVLV 110 FALE+L+ +LEGG + F +GLA + F + L+ GDHVL+ D VY R+ L Sbjct: 592 AFALEDLVTELEGGYRTRLFGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVRRVARDFLE 651 Query: 111 KNGLSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVD 170 G+ D S + ++ NTK +Y E P + L ++ DL A++ K G+L VD Sbjct: 652 AFGIEVDYF-APDGSDLPGRLQANTKMVYTEVPGSLLYELCDLPAIAALCKPRGILLAVD 710 Query: 171 NTFATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVL 230 NT+ PL LGADI + + TKYL GHSDVV G V T EA +A + G + Sbjct: 711 NTWGAGVLYRPLALGADISIMALTKYLSGHSDVVMGSVCTRQEAW-PALAAMSDTFGNTV 769 Query: 231 GPQDSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQM 290 P D++L+ RG +TL R+ H++ AL +A +L+ P+V+RV++P LP HP + L ++ Sbjct: 770 SPDDAYLVLRGARTLVPRLDTHERQALEIAHWLQAQPQVKRVFHPALPEHPGHGLWQRDF 829 Query: 291 RGFSGMLSFTLK--NDSEATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREA 348 G +G+LSF L+ +D+ F+++L++F LG S GG ESLV T A QR Sbjct: 830 NGSNGLLSFELREHDDAYLERFIDALQVFGLGASWGGFESLV------TVADTQDRQRAE 883 Query: 349 AGIRDGLVRLSVGIEHEQDLLEDLEQAFAK 378 + +VRL VG+E + L+EDL + FA+ Sbjct: 884 DRALNPVVRLHVGLEDVEVLIEDLRRGFAQ 913 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: 770 Number of extensions: 35 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: 921 Length adjustment: 37 Effective length of query: 343 Effective length of database: 884 Effective search space: 303212 Effective search space used: 303212 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: 53 (25.0 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