Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Echvi_4660 Echvi_4660 cystathionine beta-synthase
Query= BRENDA::A0A0F6AQU1 (342 letters) >FitnessBrowser__Cola:Echvi_4660 Length = 456 Score = 231 bits (588), Expect = 4e-65 Identities = 130/324 (40%), Positives = 199/324 (61%), Gaps = 9/324 (2%) Query: 1 MFNSVLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLR 60 ++NS++DTIG+TPL++L++ ++ IY K E+ NPG SVKDR A+ +I DAEK G+L+ Sbjct: 2 IYNSIIDTIGDTPLVKLNRLNKGIKGTIYVKVEYFNPGNSVKDRMAIKMIDDAEKAGILK 61 Query: 61 PGGVIVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPA-APY 119 PGG I+EGT+GNTG+GL +V A GY+ + + QS+EK D L+ +GAE++ P Sbjct: 62 PGGTIIEGTSGNTGMGLALVGIARGYKCIFTMADKQSKEKIDVLKAMGAEVVVCPTNVSP 121 Query: 120 RNPNNYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFV 179 +P +Y +A++L K PN + + NQ+DN N +AH ETT EIW+DT +I F Sbjct: 122 DDPRSYY----SVAKKLNKDIPN-SFYPNQYDNLSNWKAHYETTGPEIWKDTEGKITHFA 176 Query: 180 AAVGSGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEG--DSITEGIGQG 237 A VG+GGT++GTA LKE+N +I D +G+ + TGE +TEGIG+ Sbjct: 177 AGVGTGGTMSGTAKYLKEQNPSIVSVGIDTYGSVFKKYKETGEFDENEIYPYLTEGIGED 236 Query: 238 RITANLEGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKD-LGPGH 296 + AN++ D ++ D ++ + L EEGL +G S G + GA+ A+ L Sbjct: 237 ILPANVDFSMIDHFVKVTDKDSAVMTRRLSREEGLFVGWSCGSAVHGALEYARQHLTEQD 296 Query: 297 TIVTVLCDYGNRYQSKLFNPAFLR 320 T+V +L D+G RY K++N +++ Sbjct: 297 TMVIILPDHGTRYLGKVYNDDWMK 320 Lambda K H 0.316 0.137 0.398 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: 400 Number of extensions: 19 Number of successful extensions: 4 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: 342 Length of database: 456 Length adjustment: 31 Effective length of query: 311 Effective length of database: 425 Effective search space: 132175 Effective search space used: 132175 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