Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate N515DRAFT_4297 N515DRAFT_4297 cystathionine beta-synthase (EC 4.2.1.22)
Query= BRENDA::P35520 (551 letters) >FitnessBrowser__Dyella79:N515DRAFT_4297 Length = 456 Score = 282 bits (721), Expect = 2e-80 Identities = 172/473 (36%), Positives = 272/473 (57%), Gaps = 37/473 (7%) Query: 80 ILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPG 139 +L+ IG TPMVR ++ CEL K E N GGS+KDRI L MIE AER G +KPG Sbjct: 7 VLELIGRTPMVRAQRLDAG---SCELFLKLESANPGGSIKDRIGLSMIEGAERAGKIKPG 63 Query: 140 DTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDS 199 T++E T+GNTG+GLAL A +GYR ++V+P+KMS EK+ L+A+GAE+V T ++ Sbjct: 64 ATLVEGTAGNTGLGLALVAQQKGYRLVLVVPDKMSREKIFNLKAMGAEVVLTRSDVAKGH 123 Query: 200 PESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGG 259 PE + +A R+ E P ++ ++Q+ N NP AH TT EIL+Q DG++D +V G+ G Sbjct: 124 PEYYQDMAERIARETPGAYFINQFGNPDNPAAHIATTGPEILEQMDGRVDAIVVGCGSSG 183 Query: 260 TITGIARKLKEKCPGCRIIGVDPEGSILAE--PEELNQTEQTTYEVEGIGYDFIPTVLDR 317 T++G++R E P I+ DP GSILA+ E + T+ ++ VEGIG DF+P++ D Sbjct: 184 TMSGLSRYFAEHSPDTEIVLADPVGSILAQYINEGVLSTKSGSWMVEGIGEDFLPSISDF 243 Query: 318 TVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDS 377 + V K + +D+E+F AR L+A+EG+L G S G+ ++ A+K +E + +R V ++ D+ Sbjct: 244 SRVRKAYAISDKESFLAARELLAKEGVLGGSSTGTLLSAALKYCREQTQPKRVVTLVCDT 303 Query: 378 VRNYMTKFLSDRWMLQKGFLKEEDLTEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEI 437 Y++K +D WML GF+ E H +++L L P T T+ G E+ Sbjct: 304 GNKYLSKMYNDYWMLDNGFIDREQ---------HGDLRDL-LLRPFTQRDTVVVGPG-EL 352 Query: 438 L-----REKGFD--QAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQI 490 L R K +D Q PV+D ++G++ ++L + A + + D V + + + Sbjct: 353 LMTAYTRMKLYDVSQLPVMD-GNKLVGILDESDVLMHVHADESRFRDPVSTAMISNLQIL 411 Query: 491 RLTDTLGRLSHILEMDHFALVVHEQIQYHSTGKSSQRQMVFGVVTAIDLLNFV 543 + +++ L + E H A+V+ + G++T IDLLN++ Sbjct: 412 DIHESITALLPVFERGHVAIVM-------------DGEQFMGLITRIDLLNYL 451 Lambda K H 0.317 0.135 0.402 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: 609 Number of extensions: 31 Number of successful extensions: 3 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: 551 Length of database: 456 Length adjustment: 34 Effective length of query: 517 Effective length of database: 422 Effective search space: 218174 Effective search space used: 218174 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 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