GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Shewanella sp. ANA-3

Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate 7025489 Shewana3_2643 methionine gamma-lyase (RefSeq)

Query= BRENDA::O05394
         (379 letters)



>FitnessBrowser__ANA3:7025489
          Length = 397

 Score =  320 bits (819), Expect = 6e-92
 Identities = 173/385 (44%), Positives = 240/385 (62%), Gaps = 11/385 (2%)

Query: 2   KKKTLMIHGGITGDEKTGAVSVPIYQVSTYK--------QPKAGQHTGYEYSRTANPTRT 53
           K  T  IH G    E  G +  P+YQ +T+         +  AG   GY Y+R  NPT  
Sbjct: 10  KAATQAIHAGHER-EAFGTLVTPLYQTATFVFESAQQGGERFAGNEPGYIYTRLGNPTVA 68

Query: 54  ALEALVTELESGEAGYAFSSGMAAITAVMML-FNSGDHVVLTDDVYGGTYRVMTKVLNRL 112
            LE  +  LE  EA  A +SGM A++A ++     GDH+V ++ VYG T+ +MT    R 
Sbjct: 69  ELERKMAILEGAEAAAATASGMGAVSAALLANLQMGDHLVASNAVYGCTFALMTSQFARF 128

Query: 113 GIESTFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNT 172
           GIE T VD +    +E+AI+PNT+ I+ ETP NP L++ DL  +ADIAK+  ++ IVDNT
Sbjct: 129 GIEVTLVDFTDLAAIERAIKPNTRVIFCETPVNPHLQVFDLKGIADIAKRHQLVSIVDNT 188

Query: 173 FNTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASKELGEELHFVQNSTGGVLGP 232
           F TP  QQPL  G D+V+HSATKYL GH DV+ G+V  + ++L    + +    G V+ P
Sbjct: 189 FMTPLLQQPLAFGIDLVVHSATKYLNGHGDVIAGVVCGSEEQLHRVKYEILKDIGAVMSP 248

Query: 233 QDSWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYYPGSSNHPGHELAKTQGAG 292
            D+WL++RG+KTL +R++    +A+++A FLE HPAV  +YYPG  +H GH     Q A 
Sbjct: 249 HDAWLILRGLKTLDVRLQRHCDSAQRVAEFLEQHPAVTRVYYPGLKSHSGHRFIGGQMAK 308

Query: 293 FGGMISFDI-GSEERVDAFLGNLKLFTIAESLGAVESLISVPARMTHASIPRERRLELGI 351
            GG+I+F++  S E+  AF+G LKLF+IA SLG  ESLI  PA MTH+    E R   GI
Sbjct: 309 AGGVIAFELAASLEQAMAFVGYLKLFSIAVSLGDAESLIQHPASMTHSPYTPEARQAAGI 368

Query: 352 TDGLIRISVGIEDAEDLLEDIGQAL 376
           +D L+RIS+G+ED  D++ED+ QAL
Sbjct: 369 SDNLLRISIGLEDCGDIIEDLNQAL 393


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: 10
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: 379
Length of database: 397
Length adjustment: 30
Effective length of query: 349
Effective length of database: 367
Effective search space:   128083
Effective search space used:   128083
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