Align cystathionine β-synthase (EC 4.2.1.22) (characterized)
to candidate WP_011384252.1 AMB_RS09340 CBS domain-containing protein
Query= metacyc::MONOMER-22007 (524 letters) >NCBI__GCF_000009985.1:WP_011384252.1 Length = 455 Score = 246 bits (627), Expect = 2e-69 Identities = 151/440 (34%), Positives = 237/440 (53%), Gaps = 21/440 (4%) Query: 85 NILNKVGNTPLVRINKIGKYFGLKCELLAKCEYFNAGGSVKDRISLRMVEDAERAGILKP 144 ++L ++GNTPL+ + + C L K E N GS+KDR +L MV AER G+L+P Sbjct: 6 DLLCQIGNTPLIELTNLDT---APCRLFVKLESRNPSGSIKDRAALSMVRAAERDGLLRP 62 Query: 145 GDTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVRTPTTARFD 204 G ++E T+GNTG+ LAL AA +GYR +V+P+K ++KV LRA+GAE+V + Sbjct: 63 GGHLVEATAGNTGLALALLAAHRGYRLTLVIPDKAGLDKVSHLRAMGAEVVLARSDVPRR 122 Query: 205 SPESHVGVAWRLKNEIPNAHILDQYRNASNPLTHYDTTAEEILQQCEGKIDMLVATAGTG 264 PE + VA RL E AH +DQ+ N +NP H D T E+ +Q G++D +VA AG+G Sbjct: 123 HPEHYQNVASRLAGE-TGAHFIDQFNNPANPAAHEDGTGPELWEQMGGRVDAVVAGAGSG 181 Query: 265 GTITGISRKLKEKCPGCKIIGVDPEGSILAQPDELNKTDKT-MYEVEGIGYDFVPTVLDR 323 GT+TG+SR + P +++ DP GS+LA + + + VEGIG D +P V D Sbjct: 182 GTLTGLSRFFARRSPATEMVLADPRGSVLADYVRTGRVGEAGSWLVEGIGGDSIPMVSDF 241 Query: 324 SLVDQWYKSNDEESFALARMLIREEGLLCGGSSGSAMSVAVKAAKELKEGQRCVVIFPDS 383 S V + Y +D ESFA AR+++R EGLL G SSG+ ++ A++ +E +R + D+ Sbjct: 242 SRVTRAYSVSDRESFATARLVLRIEGLLVGSSSGTLLAAALRYCREQTAPKRVATLVCDA 301 Query: 384 IRNYMSKFLSDKWMIQKGFMTEE------DLVKKPWWWNVSVQELSLSAPLTVLPTVTCA 437 ++S+ + W+ +G + + DL+ + A +TV P T + Sbjct: 302 GNRHLSRLHDESWLADQGLLQRDEHGDLRDLISR---------RHDEGAAITVRPDDTLS 352 Query: 438 KTVEILREKGFDQVPVVDESGVILGMVTLGNMLSSLLAGKVQPSDEVSKVIYKQFKQINL 497 +R QVPVV I G++ ++L +L GK V + ++ + + Sbjct: 353 TAYNRMRVNDVSQVPVVVGDRCI-GLLDESDVLIALAEGKFGFDLPVRDAMTRKIETVTP 411 Query: 498 KDNLGRLSHILETDHFALVV 517 + RL + + A+VV Sbjct: 412 QTPPERLLPLFDRGWVAIVV 431 Lambda K H 0.316 0.134 0.399 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: 511 Number of extensions: 25 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: 524 Length of database: 455 Length adjustment: 34 Effective length of query: 490 Effective length of database: 421 Effective search space: 206290 Effective search space used: 206290 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: 52 (24.6 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