Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Ac3H11_549 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_549 Length = 458 Score = 276 bits (705), Expect = 1e-78 Identities = 173/426 (40%), Positives = 229/426 (53%), Gaps = 49/426 (11%) Query: 15 LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEH---------QGFEYSRTHNPT 65 + + TLA+H G SPDP+T AV PIY T YA S +H G Y+R NPT Sbjct: 32 MKIETLAVHAGYSPDPTTKAVAVPIYQTVAYAFDS-AQHGADLFDLKVPGNIYTRIMNPT 90 Query: 66 RFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRR 124 E+ VAALEGG A A ASGMAA T + + +AG ++V+ LYGGT+ LF Sbjct: 91 TDVLEKRVAALEGGIAALAVASGMAAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLP 150 Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVV 184 + G+ F D DPA+F I A TK ++IE+ NP+ + DIAAIA +A HG+ +V Sbjct: 151 QQ-GITTRFADPRDPASFAQHIDARTKAIFIESIGNPLGNVTDIAAIAKVAHDHGVPLIV 209 Query: 185 DNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV-------------------- 224 DNT SP L RP+ GAD+VVHS TKYL GH + VGG V Sbjct: 210 DNTVPSPYLLRPIEHGADIVVHSLTKYLGGHGNSVGGAIVDSGKFPWAEHKARFPRLNEP 269 Query: 225 ------------VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENA 272 +G A + + G P +FL L+G++TL LRM C+N Sbjct: 270 DVSYHGVVYTEALGPAAFIGRARVVPLRNTGAALSPQSAFLILQGIETLALRMDRICDNT 329 Query: 273 LALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSG-FGGIVSIVLKG----GFDAAKRF 327 LALA++L++HP +E V Y GL HP H L +RQ G GI+S LK A RF Sbjct: 330 LALAKYLQSHPKVEWVRYAGLPDHPDHALVQRQSGGKASGILSFGLKSTDADPRAAGARF 389 Query: 328 CEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRG 387 + +LFT ++G +SL HPA TH + + G+S+++VRLSVGIE + DLR Sbjct: 390 LDALQLFTRLVNIGDAKSLATHPASTTHRQLNPEELAKAGVSESMVRLSVGIEHIDDLRA 449 Query: 388 DLERAL 393 DL +AL Sbjct: 450 DLVQAL 455 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: 552 Number of extensions: 21 Number of successful extensions: 6 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: 397 Length of database: 458 Length adjustment: 32 Effective length of query: 365 Effective length of database: 426 Effective search space: 155490 Effective search space used: 155490 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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