Align cystathionine gamma-lyase; EC 4.4.1.1 (characterized)
to candidate YP_001327869.1 Smed_2201 methionine gamma-lyase
Query= CharProtDB::CH_122519 (419 letters) >NCBI__GCF_000017145.1:YP_001327869.1 Length = 427 Score = 213 bits (542), Expect = 9e-60 Identities = 139/424 (32%), Positives = 209/424 (49%), Gaps = 35/424 (8%) Query: 11 PSNGQNGDSNTHQQRQFATLAVHAGAPHDPTTGAVIAPISLSTTFAQESVGKPVGLYE-- 68 PS G+ H + TL ++ G + + GAV PI L++TF S + ++ Sbjct: 6 PSKTHIGNHKLHPE----TLMLNYGYDPELSEGAVKPPIFLTSTFVFHSAEEGRDFFDFV 61 Query: 69 ---------------YTRSSNPNRDNFEEAVASLEHAKYALAFSSG-SATTATILHSLAP 112 Y+R ++PN + E+ +A E A+ FSSG SA T+L + P Sbjct: 62 SGRREPPEGVGAGLVYSRFNHPNSEIVEDRLAIYERAEAGALFSSGMSAIATTLLAFVRP 121 Query: 113 GSHVVSVSDVYGGTHRYFTKVAAAHGVNVSF------SSCLELDVEKLIRPNETKLVWIE 166 G ++ +YGGT K G++ + + + E+ + ++ IE Sbjct: 122 GDSILHSQPLYGGTETLLAKTFLNLGISATGFADGVDEAAVSAAAEEAMSKGRVSMILIE 181 Query: 167 TPSNPTLALVDIRKVAAVAHR------HGVLVVVDNTFMSPYVQNPLDHGADVVIHSVTK 220 TP+NPT +LVD+ + +A R H +V DNT + P Q+P++HGAD+ ++S+TK Sbjct: 182 TPANPTNSLVDVAMIRRIAERIEERQAHRPIVACDNTLLGPVFQHPIEHGADLSLYSLTK 241 Query: 221 YINGHSDVLMGVAAFNSDELKERFTFLQNAIGAVPSPFDCWLAHRGLKTLHLRAREATAN 280 Y+ GHSD++ G A S L + L+ +IG P CW+ R L+TL +R +A N Sbjct: 242 YVGGHSDLIAG-AVLGSKALIRQVKALRGSIGTQLDPHSCWMIGRSLETLSVRMEKANEN 300 Query: 281 ATAVALALESSPHVISVNYPGLNSHPNREIAVKQHRKGMGGGMLSFRIKGGHKAAHLFCE 340 A VA L P V ++Y + V + G SF I GG +AA F Sbjct: 301 ARIVAEFLRDHPKVEHIHYLPFHDPEAPVGRVFAAQCTGAGSTFSFDIAGGQEAAFRFLN 360 Query: 341 YTKIFTLAESLGGVESLCEVPSSMTHAGIPKEEREAAGVYDDLVRMSCGIEDVEDLTADT 400 +IF LA SLGG ESL P++MTH+G+P E R GV + +R+S GIE +DL AD Sbjct: 361 ALQIFKLAVSLGGTESLASHPAAMTHSGVPIEVRARIGVLESTIRLSIGIEHPDDLVADV 420 Query: 401 MQAL 404 AL Sbjct: 421 ANAL 424 Lambda K H 0.316 0.130 0.377 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: 447 Number of extensions: 22 Number of successful extensions: 7 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: 419 Length of database: 427 Length adjustment: 32 Effective length of query: 387 Effective length of database: 395 Effective search space: 152865 Effective search space used: 152865 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 10 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