Align cystathionine gamma-lyase (subunit 2/2) (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate 3607379 Dshi_0793 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)
Query= BRENDA::B3TNN8 (394 letters) >FitnessBrowser__Dino:3607379 Length = 431 Score = 204 bits (518), Expect = 5e-57 Identities = 143/422 (33%), Positives = 207/422 (49%), Gaps = 50/422 (11%) Query: 3 FDTKLIHGGISEDKATGAVSVPIYM------------ASTFHQQKIGENQYEYSRSGNPT 50 FDT IH G D ATGA PIY A+ F+ Q++G Y YSR NPT Sbjct: 10 FDTLQIHAGARPDPATGARQTPIYQTTGYVFRDADHAAALFNLQEVG---YIYSRLTNPT 66 Query: 51 REAVEKLIAELEGGTAGFAFASGSAA-IDTVFSMFSAGDHFVIGNDVYGGTFRLIDAVLK 109 +++ IA LEGG +SG AA I +F + G + V+ +YGGT +K Sbjct: 67 VAVLQERIATLEGGVGAVCCSSGHAAQIMALFPLMQPGCNIVVSTRLYGGTVTQFGQTIK 126 Query: 110 RFGMTFTVVDTRDLAAVEEAITPNTKAIYLETPTNPLLRVTDIAAVAKIAKSHQILSIID 169 RFG + VD DL AV AI +T+A++ E NP + D+ A+A IA + I IID Sbjct: 127 RFGWSAKFVDFDDLDAVRAAIDDDTRAVFGEAIANPGGYIMDVRAIADIADAAGIPLIID 186 Query: 170 NTFSSPYVQRPLEQGVDIVLHSASKYLGGHSDVIAGLVVTKDD----------------- 212 NT ++PY+ RP+E G +V+HS +KYL G+ V G VV Sbjct: 187 NTTATPYLCRPIEHGATLVVHSTTKYLTGNGTVTGGCVVDSGKFDWAASGKFPSLSEPEP 246 Query: 213 -----QLAEKIGYLQNAIGGI----------LAPQESWLLQRGIKTLSLRMRAHLANAEA 257 + AE G L GI + PQ + GI+TLSLRM H+ NAE Sbjct: 247 AYHGLRFAETFGPLAFTFHGIAVGLRDLGMTMNPQGAHYTLMGIETLSLRMARHVENAEK 306 Query: 258 VFNYLSNQPLVSKIYYPGDPNNPDYEVAKKQM-HGFGAMISFELQDGLDP-KQFVEQLHV 315 + +L V + Y G P++P +E K G GA+ +F ++ G + + V+ L + Sbjct: 307 IAKWLEADDRVEFVTYAGLPSSPYFERVKTVCPRGAGALFTFAVKGGYEACIKLVDSLEI 366 Query: 316 ITLAESLGALESLIEIPALMTHGSIPRDIRLKNGIKDELIRLSVGVEDQKDLLADLERGF 375 + +LG SLI A TH + + + G ++RLS+G+ED DL+ADL++ Sbjct: 367 FSHVANLGDTRSLIIHSASTTHRQLTPEQQEAAGAAPNVVRLSIGIEDADDLIADLDQAL 426 Query: 376 NE 377 ++ Sbjct: 427 SK 428 Lambda K H 0.317 0.134 0.376 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: 413 Number of extensions: 22 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: 394 Length of database: 431 Length adjustment: 31 Effective length of query: 363 Effective length of database: 400 Effective search space: 145200 Effective search space used: 145200 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 (21.6 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