Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Pf1N1B4_4430 Cystathionine beta-lyase (EC 4.4.1.8)
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4430 Length = 919 Score = 167 bits (424), Expect = 8e-46 Identities = 106/329 (32%), Positives = 174/329 (52%), Gaps = 27/329 (8%) Query: 51 NPTRQLVEDAIANLENGARGLAFSSGMAAI-QTIMALFKSGDELIVSSDLYGGTYRLFEN 109 NPT +ED + LE G R + +G+AA+ QT +A + GD ++++ +Y RL Sbjct: 592 NPTAFALEDLVTELEGGYRTRLYGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVRRLARE 651 Query: 110 EWKKYGLTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLL 169 + +G+ Y D L++++ NTK V+ E P + L + D+ IA + K G+LL Sbjct: 652 LLEPFGIQVSYFA-PDGSGLQAQLQANTKMVYTEVPGSLLYELCDLPAIAALCKPRGILL 710 Query: 170 IVDNTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIG 229 VDNT+ + L RPL LGADI I + TKYL GH+D++ G V + E + + + + G Sbjct: 711 AVDNTWGSGYLYRPLTLGADISIMALTKYLCGHSDVVMGSVCTRQE-VWQPLSSMSDTFG 769 Query: 230 AVLPPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYP------------ 277 + P D++L++RG +TL+ R+ H+ A E+A +L+ Q ++ V +P Sbjct: 770 IAVSPDDAYLVLRGARTLAPRLDVHERQALEIAQWLQAQPQVKRVFHPALPDHPHHALWR 829 Query: 278 ----GKGGMLSFRLQKEE--WVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEI 331 G G+LSF L++ + +V F+ AL+ S GG ES +T D + Sbjct: 830 RDFNGSNGLLSFELREADATYVERFIDALQVFGLGASWGGYESLVTV------ADTKDRN 883 Query: 332 RIANGVCNRLLRFSVGIEHAEDLKEDLKQ 360 A+ N +LR +G+E + L EDL++ Sbjct: 884 SAADRALNPVLRLHIGLEDVDALIEDLQR 912 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: 761 Number of extensions: 41 Number of successful extensions: 5 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: 919 Length adjustment: 36 Effective length of query: 337 Effective length of database: 883 Effective search space: 297571 Effective search space used: 297571 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: 53 (25.0 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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