GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CBS in Dyella japonica UNC79MFTsu3.2

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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