Align cystathionine beta-synthase; EC 4.2.1.22 (characterized)
to candidate 16513 b2414 cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI)
Query= CharProtDB::CH_122414 (533 letters) >FitnessBrowser__Keio:16513 Length = 323 Score = 219 bits (559), Expect = 9e-62 Identities = 137/313 (43%), Positives = 183/313 (58%), Gaps = 16/313 (5%) Query: 21 IGNTPLVRLNKLPQNLGINATVYAKLEYFNAGGSVKDRIALRMIEEAERSGRIKPGDTLI 80 IG+TPLVRLN++ N + AK+E N SVK RI MI +AE+ G +KPG L+ Sbjct: 12 IGHTPLVRLNRIG-----NGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLKPGVELV 66 Query: 81 EPTSGNTGIGLALVAAVKGYKTIITLPEKMSAEKVSVLRALNATIIRTPNEAAYDS--PE 138 EPTSGNTGI LA VAA +GYK +T+PE MS E+ +L+AL A ++ T + Sbjct: 67 EPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGMKGAIQK 126 Query: 139 SHIGVAKRLEKELPNAHILDQYGNENNPLAHELGTAQEIWSQTKGQIKAIVAGAGTGGTI 198 + VA EK L +L Q+ N NP HE T EIW T GQ+ +AG GTGGT+ Sbjct: 127 AEEIVASNPEKYL----LLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGGTL 182 Query: 199 TGLSRGLK--KHNSNVQVIAADPQGSILALPAALNEEHANEPYKVEGIGYDFIPQVLDQH 256 TG+SR +K K +++ +A +P S + A EE P+K++GIG FIP LD Sbjct: 183 TGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLDLK 242 Query: 257 AVDKWYKTDDKESFQYARRLIAEEGLLVGGSSGSAIAALVKAARDNMFKEGDVVVVILPD 316 VDK ++E+ ARRL+ EEG+L G SSG+A+AA +K D F + +VVILP Sbjct: 243 LVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKN-IVVILPS 301 Query: 317 SIRSYLTK--FAD 327 S YL+ FAD Sbjct: 302 SGERYLSTALFAD 314 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: 329 Number of extensions: 15 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: 533 Length of database: 323 Length adjustment: 31 Effective length of query: 502 Effective length of database: 292 Effective search space: 146584 Effective search space used: 146584 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: 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