Align cystathionine beta-synthase; EC 4.2.1.22 (characterized)
to candidate AO356_28790 AO356_28790 cysteine synthase
Query= CharProtDB::CH_122414 (533 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28790 Length = 347 Score = 169 bits (428), Expect = 2e-46 Identities = 115/333 (34%), Positives = 176/333 (52%), Gaps = 27/333 (8%) Query: 14 LDSITQHIGNTPLVRLNKLPQNLGINATVYAKLEYFNAGGSVKDRIALRMIEEAERSGRI 73 L+ ++ IGNTP++ ++ +P +A + K+E N GGS+KDR+A M+ A +SGR+ Sbjct: 3 LNKVSDLIGNTPMLGID-IPDT---HARLLLKIEKNNPGGSIKDRMARNMVLAALKSGRL 58 Query: 74 KPGDTLIEPTSGNTGIGLALVAAVKGYKTIITLPEKMSAEKVSVLRALNATIIRTPNEAA 133 KPG ++E +SGNTGIGLA+ A G I + + +K++V++AL A + A Sbjct: 59 KPGGVVVESSSGNTGIGLAMAAVEFGLHFIAVVDHHAAQDKIAVMKALGADV----RFVA 114 Query: 134 YDSPESHIGVAKR------LEKELPNAHILDQYGNENNPLAHELGTAQEIWSQTKGQIKA 187 E + V +R L +++P A ++Q N N + +E +Q +G++ A Sbjct: 115 GHYREDEVAVVERQRMAAELAQQIPGAVFMNQSDNAANAGGYS-DFVRETIAQVEGKVGA 173 Query: 188 IVAGAGTGGTITGLSRGLKKHNSNVQVIAADPQGSILALPAALNEEHANEPYKVEGIGY- 246 V GTGG++TG++RGLK HN + +A +P GSI+ H PY G G Sbjct: 174 YVGCVGTGGSMTGIARGLKLHNPDTVTVAVEPAGSIVF-------GHPGYPYYQSGTGTP 226 Query: 247 --DFIPQVLDQHAVDKWYKTDDKESFQYARRLIAEEGLLVGGSSGSAIAALVKAARDNMF 304 D + VLD +D + D ++F+ AR + GLLVGGS+G AI ++ + Sbjct: 227 AGDTVGLVLDYSCIDLGVQVTDSQAFETARYIARNLGLLVGGSTGGAIFKALEFIHKGVL 286 Query: 305 KEGDVVVVILPDSIRSYLTKFADDDWLAANDLL 337 G+VVV I D YL DD WL DLL Sbjct: 287 -TGNVVVPI-ADGGEKYLHTVFDDQWLQERDLL 317 Lambda K H 0.314 0.131 0.372 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: 397 Number of extensions: 22 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: 533 Length of database: 347 Length adjustment: 32 Effective length of query: 501 Effective length of database: 315 Effective search space: 157815 Effective search space used: 157815 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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