Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate SMc01809 SMc01809 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::Q96VU7 (417 letters) >FitnessBrowser__Smeli:SMc01809 Length = 426 Score = 203 bits (517), Expect = 7e-57 Identities = 137/422 (32%), Positives = 207/422 (49%), Gaps = 42/422 (9%) Query: 21 GFGTLAVHAGSPHDPATGAVIEAISLSTTFAQTAVGKPVGEFE-------YSRSSNPNRA 73 GF TLA+HAG+ DP TGA I +T+F F Y+R NP +A Sbjct: 6 GFSTLAIHAGAQPDPTTGARATPIYQTTSFVFNDTDHAAALFGLQQFGNIYTRIMNPTQA 65 Query: 74 NFEKMVAALEHAKYALAYSSGSATTANILQSLAA-GSHVISVSDVYGGTHRYFTQVAKAH 132 E+ +AALE LA SSG A + ++ G + +S +YGG+ F KA Sbjct: 66 VLEERIAALEGGTAGLAVSSGHAAQLLVFHTIMRPGDNFVSARQLYGGSANQFGHAFKAF 125 Query: 133 GVKVTFTPEIEVDIRD-HITDATKLVWIETPSNPTLRLVDIRAVATAAHERGILVVVDNT 191 +V + E + D I + TK ++IE+ +NP VDI A+A A G+ ++VDNT Sbjct: 126 DWQVRWADSAEPESFDAQIDERTKAIFIESLANPGGTFVDIAAIADVARRHGLPLIVDNT 185 Query: 192 FLSPYVQNPLDHGADIVVHSVTKYINGHSDVVMGVAA------FNSDELYARLSFLQNAI 245 +PY+ PL+HGADIVVHS+TK+I GH + + G+ ++ Y LS + Sbjct: 186 MATPYLMRPLEHGADIVVHSLTKFIGGHGNSMGGIIVDGGTFDWSKSGKYPLLSEPRPEY 245 Query: 246 GAVP--------------------------SAFDSWLAHRGAKTLHLRAREATTNATAIA 279 G V S F+++L G +TL LR + NA +A Sbjct: 246 GGVVLHQAFGNFAFAIAARVLGLRDFGPAISPFNAFLIQTGVETLPLRMQRHCDNALEVA 305 Query: 280 HALEASPLVISVNYPGLESHPHRAIALKQHRNGMGGGMLSFRIHGGHAAAEKFCQYTKIF 339 L+ V V Y GLE P+ A+ + G G + +F + GG+ A ++F + ++F Sbjct: 306 KWLKGHEKVSWVRYSGLEDDPNHALQKRYSPKG-AGAVFTFGLAGGYEAGKRFVEALEMF 364 Query: 340 TLAESLGGVESLCEIPSSMTHAGIPKAQREAVGIFDDLVRISCGVEDAEDLKADVLQALE 399 + ++G SL P+S TH + Q+ A G D++R+S G+ED D+ AD+ QAL Sbjct: 365 SHLANIGDTRSLVIHPASTTHRQLTPEQQVAAGAGPDVIRLSVGIEDVADIIADLEQALG 424 Query: 400 RA 401 +A Sbjct: 425 KA 426 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: 536 Number of extensions: 29 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: 417 Length of database: 426 Length adjustment: 32 Effective length of query: 385 Effective length of database: 394 Effective search space: 151690 Effective search space used: 151690 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 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