Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_066917961.1 ACG33_RS00985 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q96VU7 (417 letters) >NCBI__GCF_001579945.1:WP_066917961.1 Length = 424 Score = 195 bits (495), Expect = 2e-54 Identities = 136/421 (32%), Positives = 205/421 (48%), Gaps = 45/421 (10%) Query: 24 TLAVHAGSPHDPATGAVIEAISLSTTFAQTAVGKPVGEFE-------YSRSSNPNRANFE 76 T+A+H G DP T +V I + + F Y+R NP E Sbjct: 5 TIAIHGGYETDPTTRSVAPPIYQTVAYEFDNAQHGADLFNLAVPGNIYTRIMNPTCDVLE 64 Query: 77 KMVAALEHAKYALAYSSGSATTANILQSLA-AGSHVISVSDVYGGTHRYFTQVAKAHGVK 135 K VA LE +LA S+G A + +LA AG +++SV +YGGT+ F + G++ Sbjct: 65 KRVAMLEGGVGSLALSAGMAAVHYAIINLAEAGDNIVSVPQLYGGTYTLFAHMLPKMGIE 124 Query: 136 VTFTPEIEVDIRDHITDA-TKLVWIETPSNPTLRLVDIRAVATAAHERGILVVVDNTFLS 194 F + + + DA TK ++ E+ NP +VD+ AVA A G+ +VDNT + Sbjct: 125 TRFAADDSAAAIEKLIDAKTKAIFFESIGNPAGNIVDVEAVAKMARGHGVATIVDNTVAT 184 Query: 195 PYVQNPLDHGADIVVHSVTKYINGHSDVVMGVAA----------------FNS-DELY-- 235 P + P+D+G DIVVH++TKY+ GH + G+ FN +E Y Sbjct: 185 PSLLKPIDYGIDIVVHALTKYMGGHGTTLGGLIVDSGNFPWADHQQRYPMFNEPEEAYHG 244 Query: 236 ---------------ARLSFLQNAIGAVPSAFDSWLAHRGAKTLHLRAREATTNATAIAH 280 AR L+N GA S F+++ +G +TL LR NA +A Sbjct: 245 VVYVDALGPAAYIGRARTVPLRNT-GAALSPFNAFQLLQGIETLPLRMERHCENAQRVAE 303 Query: 281 ALEASPLVISVNYPGLESHPHRAIALKQHRNGMGGGMLSFRIHGGHAAAEKFCQYTKIFT 340 L+ +V V+Y GL++HPH A+A K + G G+L+F + GG A KF K+F Sbjct: 304 HLQEHAMVEWVSYAGLKNHPHHALAQK-YMKGRASGILTFGVKGGFDAGVKFYDALKLFK 362 Query: 341 LAESLGGVESLCEIPSSMTHAGIPKAQREAVGIFDDLVRISCGVEDAEDLKADVLQALER 400 ++G +SL P+S TH + + Q+ VG+ + +R+S G+E EDL D+ QAL Sbjct: 363 RLVNIGDAKSLACHPASTTHRQLTEQQQREVGVAPEAIRLSIGIEAIEDLLEDLDQALSV 422 Query: 401 A 401 A Sbjct: 423 A 423 Lambda K H 0.317 0.130 0.378 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: 525 Number of extensions: 32 Number of successful extensions: 6 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: 417 Length of database: 424 Length adjustment: 32 Effective length of query: 385 Effective length of database: 392 Effective search space: 150920 Effective search space used: 150920 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 10 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