GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Bacteroides thetaiotaomicron VPI-5482

Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate 351451 BT1923 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)

Query= BRENDA::O05394
         (379 letters)



>FitnessBrowser__Btheta:351451
          Length = 426

 Score =  224 bits (570), Expect = 5e-63
 Identities = 149/420 (35%), Positives = 222/420 (52%), Gaps = 46/420 (10%)

Query: 2   KKKTLMIHGGITGDEKTGAVSVPIYQVSTYKQPKAGQ--------HTGYEYSRTANPTRT 53
           K +TL +  G T  +    V +PIYQ +T+K   + Q         +GY Y+R  NPT  
Sbjct: 6   KPETLCVQAGWTPKKGEPRV-LPIYQSTTFKYDTSEQMARLFDLEDSGYFYTRLQNPTND 64

Query: 54  ALEALVTELESGEAGYAFSSGMAA-ITAVMMLFNSGDHVVLTDDVYGGTYRVMTKVLNRL 112
           A+ A +  LE G A    SSG AA   A+  +  +GDH V +  +YGGT+ +    + +L
Sbjct: 65  AVAAKIAALEGGVAAMLTSSGQAANFYAIFNICQAGDHFVCSSAIYGGTFNLFGVTMKKL 124

Query: 113 GIESTFVDT-SSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDN 171
           GI+ TFV+  +S EE+  A +PNTKA++ ET +NP L++ D+   A IA   GV LIVDN
Sbjct: 125 GIDVTFVNPDASEEEISAAFQPNTKALFGETISNPSLEVLDIEKFARIAHSHGVPLIVDN 184

Query: 172 TFNTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVV---------------------- 209
           TF TP   +P   GADI++HS TKY+ GH+  VGG +V                      
Sbjct: 185 TFPTPINCRPFEWGADIIVHSTTKYMDGHATSVGGCIVDSGNFDWDAHADKFPGLCTPDE 244

Query: 210 -----TASKELGEELHFVQNST------GGVLGPQDSWLLMRGIKTLGLRMEAIDQNARK 258
                T +K  G+  +  + +       G +  PQ+S+LL  G++TL LRM    +NA+K
Sbjct: 245 SYHGLTYTKAFGKGAYITKATAQLMRDLGSIQSPQNSFLLNLGLETLHLRMPQHCRNAQK 304

Query: 259 IASFLENHPAVQTLYYPGSSNHPGHELA-KTQGAGFGGMISFDI-GSEERVDAFLGNLKL 316
           +A +L  +  V  + Y G  ++  + LA K    G  G+ISF + G  +    F+ +L+ 
Sbjct: 305 VAEYLSKNEKVAWVNYCGLPDNKYYALAQKYMPNGSCGVISFGLKGGRDVSIKFMDSLEF 364

Query: 317 FTIAESLGAVESLISVPARMTHASIPRERRLELGITDGLIRISVGIEDAEDLLEDIGQAL 376
             I   +    S +  PA  TH  +  E+ +E G+   LIR+SVGIE+A+D++ DI QAL
Sbjct: 365 IAIVTHVADARSCVLHPASHTHRQLSDEQLMEAGVRPDLIRLSVGIENADDIIADIEQAL 424


Lambda     K      H
   0.316    0.134    0.375 

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: 390
Number of extensions: 23
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 379
Length of database: 426
Length adjustment: 31
Effective length of query: 348
Effective length of database: 395
Effective search space:   137460
Effective search space used:   137460
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: 50 (23.9 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