Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Pf1N1B4_4430 Cystathionine beta-lyase (EC 4.4.1.8)
Query= metacyc::HP_RS00540-MONOMER (380 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4430 Length = 919 Score = 233 bits (594), Expect = 2e-65 Identities = 143/390 (36%), Positives = 225/390 (57%), Gaps = 22/390 (5%) Query: 2 RMQTKLIHGGISEDATTG-AVSVPIYQTSTYRQDAIGRHKG----------YEYSRSGNP 50 R++T+L+H +E + G AV+VP+ + ST D + + + Y GNP Sbjct: 534 RIRTRLVHSARTEKGSGGRAVNVPVTRLSTVLFDNLAQMRDARARRDSERVLSYGARGNP 593 Query: 51 TRFALEELIADLEGGVKGFAFASGLAGIHAVF-SLLQSGDHVLLGDDVYGGTFRLFNQVL 109 T FALE+L+ +LEGG + + +GLA + F + L+ GDHVL+ D VY RL ++L Sbjct: 594 TAFALEDLVTELEGGYRTRLYGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVRRLARELL 653 Query: 110 VKNGLSCTIIDTSDISQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIV 169 G+ + D S ++ ++ NTK +Y E P + L ++ DL A++ K G+L V Sbjct: 654 EPFGIQVSYF-APDGSGLQAQLQANTKMVYTEVPGSLLYELCDLPAIAALCKPRGILLAV 712 Query: 170 DNTFATPYYQNPLLLGADIVAHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGV 229 DNT+ + Y PL LGADI + TKYL GHSDVV G V T E + Q ++ + G Sbjct: 713 DNTWGSGYLYRPLTLGADISIMALTKYLCGHSDVVMGSVCTRQE-VWQPLSSMSDTFGIA 771 Query: 230 LGPQDSWLLQRGIKTLGLRMEAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQ 289 + P D++L+ RG +TL R++ H++ AL +A++L+ P+V+RV++P LP HP++ L ++ Sbjct: 772 VSPDDAYLVLRGARTLAPRLDVHERQALEIAQWLQAQPQVKRVFHPALPDHPHHALWRRD 831 Query: 290 MRGFSGMLSFTLKN-DSEAV-AFVESLKLFILGESLGGVESLVGIPAFMTHACIPKTQRE 347 G +G+LSF L+ D+ V F+++L++F LG S GG ESLV T A Sbjct: 832 FNGSNGLLSFELREADATYVERFIDALQVFGLGASWGGYESLV------TVADTKDRNSA 885 Query: 348 AAGIRDGLVRLSVGIEHEQDLLEDLEQAFA 377 A + ++RL +G+E L+EDL++ FA Sbjct: 886 ADRALNPVLRLHIGLEDVDALIEDLQRGFA 915 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: 758 Number of extensions: 33 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: 380 Length of database: 919 Length adjustment: 37 Effective length of query: 343 Effective length of database: 882 Effective search space: 302526 Effective search space used: 302526 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 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