Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_012102527.1 CKL_RS10715 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000016505.1:WP_012102527.1 Length = 428 Score = 204 bits (520), Expect = 3e-57 Identities = 133/399 (33%), Positives = 199/399 (49%), Gaps = 46/399 (11%) Query: 23 VPIYQTSTYRQDAIG--------HHKGYEYSRSGNPTRFALEELIADLEGGVKGFAFASG 74 VPI Q++T++ + GY YSR NPT + + IAD+E G +SG Sbjct: 25 VPIIQSTTFKYNTSEDMGKLFDLEASGYFYSRLQNPTNDYVAQKIADMESGTAAMLTSSG 84 Query: 75 -LAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIIDTSDLSQ-IKKAIK 132 A A+F++ GDH++ +YGGTF L + + K G++ T + + + A + Sbjct: 85 QAANFFALFNICNCGDHIVASSSIYGGTFNLISVTMSKMGITTTFVSPDCTEEELNAAFQ 144 Query: 133 PNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLLLGADIVVHS 192 NTKA++ ET +NP L + D+ + A A H + IVDNTF TP P GADIV HS Sbjct: 145 TNTKAVFGETIANPALTVLDIEKFAKAAHAHDVPLIVDNTFPTPINCRPFEWGADIVTHS 204 Query: 193 GTKYLGGHSDVVAGLVT---------------------------TNNEALAQEIAFFQNA 225 TKY+ GH V G++ T E +E AF Sbjct: 205 TTKYMDGHGAAVGGVIVDSGNFDWMAHADKFPGLCTPDDSYHGITYAEKFGKEGAFITKC 264 Query: 226 -------IGGVLGPQDSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLP 278 G + PQ +++L G+++L +RM H +N VAEFL+ HPKV V Y GLP Sbjct: 265 TAQLMRDFGSIQSPQHAFILNLGLESLHVRMPRHCENGQAVAEFLQNHPKVAYVNYCGLP 324 Query: 279 THPNYELAKKQM-RGFSGMLSFTLKND-SEATPFVESLKLFILGESLGGVESLVGVPAFM 336 Y++A+K + G G++SF LK EA F+++LKL + + S PA Sbjct: 325 GDKYYKIAQKYLPNGSCGVVSFGLKGGREEAEIFMKNLKLVAIETHVADARSCCLNPATS 384 Query: 337 THACIPKTQREAAGIRDGLVRLSVGIEHEQDLLEDLEQA 375 TH + + + AG+ L+R+S GIE ++DL+ D+ Q+ Sbjct: 385 THRQMNDEELKEAGVPAELIRISCGIEDKEDLIYDISQS 423 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: 424 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 380 Length of database: 428 Length adjustment: 31 Effective length of query: 349 Effective length of database: 397 Effective search space: 138553 Effective search space used: 138553 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 Jul 25 2024. The underlying query database was built on Jul 25 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