Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 5210267 Shew_2710 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__PV4:5210267 Length = 429 Score = 219 bits (558), Expect = 1e-61 Identities = 148/427 (34%), Positives = 216/427 (50%), Gaps = 50/427 (11%) Query: 15 LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEH---------QGFEYSRTHNPT 65 + L +LA+H G + + +T A PIY T++Y +H G Y+R NPT Sbjct: 1 MKLESLALHHGYTSEATTKAAAVPIYQTTSYTFDDT-QHGADLFDLKVAGNIYTRIMNPT 59 Query: 66 RFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRR 124 E+ +AA+EGG A A ASGMAA T + L G ++V+ LYGGT+ LF Sbjct: 60 TDVLEQRLAAIEGGIGALALASGMAAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTLP 119 Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVV 184 R G++ D +A I TK ++ E+ NP +VDIA +A IA +HG+ +V Sbjct: 120 RQ-GVEVRMAAFDDFDGLEAHIDDKTKALFCESIGNPAGNIVDIARLAEIAHRHGVPLIV 178 Query: 185 DNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQ---------- 234 DNT A+P+L RP GAD+V+HS TKY+ GH +GG+ + + A Q Sbjct: 179 DNTVATPVLCRPFEHGADIVIHSLTKYIGGHGTTIGGVIIDSGKFDWAAQPQRFALLNEP 238 Query: 235 ---------------MAFL-------QNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENA 272 AF+ + G P +FL L+GL+TL LRM HC+NA Sbjct: 239 DPSYHGVVYTQAFGPAAFIGRCRVVPLRNTGAALSPQSAFLLLQGLETLALRMERHCDNA 298 Query: 273 LALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSG-FGGIVSIVLKG-GFDAAK----R 326 LALA +LE P + V Y L + P ++ SG GI+S +K +AAK R Sbjct: 299 LALANFLEQDPRVSWVNYGALDNSPYRDNCEKITSGKASGIISFGIKAEDSEAAKAAGGR 358 Query: 327 FCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLR 386 F + ++ ++G +SL HPA TH + + G+S+ L+R+SVGIE + D+ Sbjct: 359 FIDALQMILRLVNIGDAKSLACHPATTTHRQLNGEELAKAGVSEDLIRISVGIEHIEDII 418 Query: 387 GDLERAL 393 D+ +AL Sbjct: 419 ADVSQAL 425 Lambda K H 0.320 0.134 0.391 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: 501 Number of extensions: 25 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: 397 Length of database: 429 Length adjustment: 31 Effective length of query: 366 Effective length of database: 398 Effective search space: 145668 Effective search space used: 145668 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 (21.8 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