Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Pf1N1B4_4890 Cystathionine gamma-lyase (EC 4.4.1.1)
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4890 Length = 393 Score = 306 bits (783), Expect = 8e-88 Identities = 165/392 (42%), Positives = 241/392 (61%), Gaps = 27/392 (6%) Query: 1 MSQHVET--------KLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNP 52 MSQH ET ++ G D TG + PIY ++ Y + G GFDY R+ NP Sbjct: 1 MSQHDETAAPRGFATRVIHAGQTPDPSTGALMPPIYANSTYLQQSPGVHKGFDYGRSHNP 60 Query: 53 TRQLVEDAIANLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWK 112 TR +E +A+LE G R AF+SG+AAI ++ L +G ++ +DLYGGT+RLF+ + Sbjct: 61 TRFALERCVADLEGGTRAFAFASGLAAIANVLELLDAGAHIVSGNDLYGGTFRLFDKVRR 120 Query: 113 KY-GLTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIV 171 + G F + D +D + + +T+ V+VETP+NPL+ D++ +ARI ++ G++ + Sbjct: 121 RSAGHRFSFVDLTDLAAFEAALEDDTRMVWVETPSNPLLSLTDLDAVARICRQRGIICVA 180 Query: 172 DNTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVV-KDERLGEEMFQHQNAIGA 230 DNTF +P +QRPLELG DIV+HS TKYL GH+D++ G+ VV ++ L E + QNA+GA Sbjct: 181 DNTFASPWIQRPLELGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELAERLGFLQNAVGA 240 Query: 231 VLPPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------- 279 + PFD++L +RG+KTL+LRM +H +NA ELA +LE Q +++ V YPG Sbjct: 241 IAGPFDAFLTLRGVKTLALRMERHCSNALELAQWLERQPQVARVYYPGLPSHPQHELARR 300 Query: 280 -----GGMLSFRLQKE-EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRI 333 GGM+S L + FL++++ AESLGGVES I +PA TH IP E R Sbjct: 301 QMRGFGGMISLDLNSDLAGAKRFLESVRIFALAESLGGVESLIEHPAIMTHASIPVETRA 360 Query: 334 ANGVCNRLLRFSVGIEHAEDLKEDLKQALCQV 365 G+ + L+R SVG+E EDL+ DL QAL ++ Sbjct: 361 QLGIGDALVRLSVGVEDVEDLRADLAQALMRI 392 Lambda K H 0.319 0.135 0.392 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: 380 Number of extensions: 20 Number of successful extensions: 4 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: 373 Length of database: 393 Length adjustment: 30 Effective length of query: 343 Effective length of database: 363 Effective search space: 124509 Effective search space used: 124509 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