Align Cystathionine beta-synthase; Beta-thionase; Hemoprotein H-450; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate GFF1378 PGA1_c13950 cysteine synthase CysK
Query= SwissProt::P32232 (561 letters) >FitnessBrowser__Phaeo:GFF1378 Length = 344 Score = 208 bits (529), Expect = 3e-58 Identities = 130/326 (39%), Positives = 188/326 (57%), Gaps = 11/326 (3%) Query: 72 KILPDILRKIGNTPMVRINRISKNAGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERAG 131 +I D+ IG+TP++R+NR+S G CE+L K EF N G SVKDR +L +I+DA G Sbjct: 2 RIAHDLADAIGHTPLIRLNRVSDETG--CEILGKAEFMNPGQSVKDRAALYIIKDAIARG 59 Query: 132 TLKPGDTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVRTPTN 191 LKPG TI+E T+GNTGIGLAL A G++ +IV+PE S EK D+LR GA++V+ P Sbjct: 60 DLKPGGTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGAQLVQVPA- 118 Query: 192 ARFDSPESHVGVAWRLKNEI----PNSHI-LDQYRNASNPLAHYDDTAEEILQQCDGKVD 246 A + +P + V + RL E+ PN I +Q+ N +N AH + TA EI +Q GKVD Sbjct: 119 APYRNPNNFVRYSERLAKELAKTEPNGAIWANQFDNVANRQAHVETTAPEIWEQTGGKVD 178 Query: 247 MLVASAGTGGTITGIARKLKEKCPGCKIIGVDPEGSILAEPEELNQTEQTAYEV-EGIGY 305 V + G+GGT+ G+A L+ K G KI DP G+ L + + EGIG Sbjct: 179 GFVCAVGSGGTLAGVADALQPK--GVKIGLADPMGAALYSYYTTGEIATEGGSIAEGIGQ 236 Query: 306 DFIPTVLDRAVVDRWFKSNDDDSFAFARMLISQEGLLCGGSSGSAMAVAVKAAQELKEGQ 365 I L+ D ++ D D+ + L+ +EGL+ GGSS +A AV+ A+++ G+ Sbjct: 237 VRITKNLEGFKPDFCYQIEDRDALPYVFDLLHEEGLVLGGSSAINIAGAVRMAKDMGPGK 296 Query: 366 RCVVILPDSVRNYMSKFLSDKWMLQK 391 V +L D Y SK + ++ +K Sbjct: 297 TIVTVLCDYGTRYQSKLFNPDFLREK 322 Lambda K H 0.317 0.134 0.401 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: 474 Number of extensions: 25 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: 561 Length of database: 344 Length adjustment: 32 Effective length of query: 529 Effective length of database: 312 Effective search space: 165048 Effective search space used: 165048 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: 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