Align cystathionine-gamma-lyase [Acremonium chrysogenum] (characterized)
to candidate Dsui_0429 Dsui_0429 cystathionine beta-lyase/cystathionine gamma-synthase
Query= CharProtDB::CH_124009 (426 letters) >FitnessBrowser__PS:Dsui_0429 Length = 382 Score = 239 bits (611), Expect = 8e-68 Identities = 152/402 (37%), Positives = 216/402 (53%), Gaps = 28/402 (6%) Query: 9 QAPAVAAVAHQQQQQQQQSSRGFATRAVHAGSSPDPTTGAVIPAISLSTTFRQSAPSQPV 68 Q+PAV ++A + T+A D T ++P + L+TTF ++ Sbjct: 3 QSPAVPSLAPE-------------TQAARGTVPVDSTYRDIVPPLHLATTFERAGDGSYP 49 Query: 69 GLYEYSRSANPNRDNFEEAVASLENARHGFAFSSGSATTAVVLQSLASGSHVISVSDVYG 128 G YSR +P D E + LE F+SG A + VLQ+L G+ V++ +Y Sbjct: 50 GGRVYSRDGSPAYDGPEALLKELEGGAAAALFASGMAAASAVLQALKPGARVVAPRAMYW 109 Query: 129 GTHRYFTQVAQAHNIEVTFSHDIVADVGSQIRPDTKLIWIESPSNPTLSLVDIRAVADAA 188 + Q A + + F D A++ + ++ L+W+E+P+NPT + DI A A AA Sbjct: 110 ALRNWMIQFAANWQLTLEFFADD-AELAALLQRPADLVWLETPANPTWEITDIAAAAKAA 168 Query: 189 HARGVLVVVDNTFLSPYIQNPLNLGADIVVHSVTKYINGHSDVVMG-VAACNDDALASRL 247 HA G +VVD+T +P PL LGAD+V+HS TKY+NGHSDVV G + +D R+ Sbjct: 169 HAAGARLVVDSTVPTPVFTRPLELGADVVMHSATKYLNGHSDVVAGALVTRTEDDFWQRI 228 Query: 248 RFLQNAIGAVPSAFDSWLAHRGLKTLHLRAREASRNAAAVAAFLETSPYVISVNYPGLES 307 + ++ GAV F++WL RG++TL R R A+ +AAA+A+ V V YPGL S Sbjct: 229 KTVRALGGAVLGPFEAWLLARGMRTLFPRVRTAAASAAAIASHFHGHAKVGLVLYPGLPS 288 Query: 308 HPQRDIARRQHRDGMGGGMLSFRVKGGLVAADSFCSTTRVFTLAESLGGVESLVELPSVM 367 HP +A RQ + G G MLS R+ GG AA + + +VF A SLG VESLVE Sbjct: 289 HPGHAVAARQMQGGF-GAMLSLRIAGGEAAAKAVAARLQVFQRATSLGSVESLVE----- 342 Query: 368 THAGIPRQSREAVGIY--DDLIRISCGIEEAEDLVADVRQAL 407 R S E G + DDL+R+S GIE DL+AD+ QAL Sbjct: 343 -----HRASVEGPGTFCPDDLLRLSVGIEATADLIADLEQAL 379 Lambda K H 0.316 0.129 0.366 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: 390 Number of extensions: 19 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: 426 Length of database: 382 Length adjustment: 31 Effective length of query: 395 Effective length of database: 351 Effective search space: 138645 Effective search space used: 138645 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 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