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 HSERO_RS18310 HSERO_RS18310 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::B3TNN8 (394 letters) >FitnessBrowser__HerbieS:HSERO_RS18310 Length = 429 Score = 226 bits (575), Expect = 1e-63 Identities = 146/417 (35%), Positives = 221/417 (52%), Gaps = 45/417 (10%) Query: 2 EFDTKLIHGGISEDKATGAVSVPIY--MASTFHQQKIGENQYE-------YSRSGNPTRE 52 +F+T +HGG D T AV+VPIY +A F + G + ++ YSR NPT++ Sbjct: 8 KFETISVHGGYDPDPTTRAVAVPIYQTVAFAFDDTQHGADLFDLKVQGNIYSRIMNPTQD 67 Query: 53 AVEKLIAELEGGTAGFAFASGSAAID-TVFSMFSAGDHFVIGNDVYGGTFRLIDAVLKRF 111 +EK +A LEGG A ASG AA+ + ++ AGD+ V + +YGGT+ L L ++ Sbjct: 68 VLEKRLAALEGGIGALALASGQAAVTYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLPQY 127 Query: 112 GMTFTVVDTRDLAAVEEAITPNTKAIYLETPTNPLLRVTDIAAVAKIAKSHQILSIIDNT 171 G+ D R A+ E I TKAIY+E+ NPL +TDIAAVA IA H + I+DNT Sbjct: 128 GVQTRFADPRQPASFEPLIDDRTKAIYIESIGNPLGNITDIAAVADIAHRHGVPLIVDNT 187 Query: 172 FSSPYVQRPLEQGVDIVLHSASKYLGGHSDVIAGLVV-------TKDDQLAEKI------ 218 ++PY+ RP E G DIV+HS +KYLGGH + G +V K Q +++ Sbjct: 188 VATPYLLRPFEHGADIVVHSLTKYLGGHGTTLGGAIVDSGKFPWAKHKQRFKRLNEPDVS 247 Query: 219 -------------GYLQNA-------IGGILAPQESWLLQRGIKTLSLRMRAHLANAEAV 258 Y+ A +G L+P ++ + +GI+TL LR+ AN AV Sbjct: 248 YHGVVYTEALGEAAYIGRARVVPLRNMGAALSPFNAFQILQGIETLGLRLDRITANTLAV 307 Query: 259 FNYLSNQPLVSKIYYPGDPNNPDYEVAKKQMHG-FGAMISFELQDGLD-PKQFVEQLHVI 316 YL P V + Y G ++PD+ +A+ G +++F + +G + +F + L + Sbjct: 308 AQYLKRHPKVRWVNYAGLEDHPDHALAQTYFKGRASGVLTFGVANGREGGARFQDALQLF 367 Query: 317 TLAESLGALESLIEIPALMTHGSIPRDIRLKNGIKDELIRLSVGVEDQKDLLADLER 373 T ++G +SL PA TH + K G+ ++ +RLS+G+E DLLADLE+ Sbjct: 368 TRLVNIGDAKSLATHPASTTHRQLSPTELEKAGVTEDTVRLSIGIEHIDDLLADLEQ 424 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: 454 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 394 Length of database: 429 Length adjustment: 31 Effective length of query: 363 Effective length of database: 398 Effective search space: 144474 Effective search space used: 144474 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