GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CBS in Escherichia coli BW25113

Align Putative cystathionine beta-synthase MT1108; EC 4.2.1.22; Beta-thionase; Serine sulfhydrase (uncharacterized)
to candidate 16520 b2421 cysteine synthase B (O-acetylserine sulfhydrolase B) (NCBI)

Query= curated2:P9WP50
         (464 letters)



>FitnessBrowser__Keio:16520
          Length = 303

 Score =  204 bits (518), Expect = 4e-57
 Identities = 117/298 (39%), Positives = 173/298 (58%), Gaps = 14/298 (4%)

Query: 7   ISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGT 66
           + + IG TPLV+L  + PD    V  K+E  NP GS KDR A+ MI  AE  G++KPG  
Sbjct: 4   LEQTIGNTPLVKLQRMGPDNGSEVWLKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDV 63

Query: 67  IVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPA 126
           ++E TSGNTG+ LA++A  +GY+   + PD +S+++R  + AYGAE+++           
Sbjct: 64  LIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELIL---VTKEQGME 120

Query: 127 SYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTI 186
               ++  +    +G    DQ+ NP+ P +HY TTGPEIW  T G++THFV+ +GT GTI
Sbjct: 121 GARDLALEMANRGEGKLL-DQFNNPDNPYAHYTTTGPEIWQQTGGRITHFVSSMGTTGTI 179

Query: 187 TGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEIIA 245
           TG  R+++E S   V IVG  P EGS   G    P        ++ P  ++ S+ DE++ 
Sbjct: 180 TGVSRFMREQS-KPVTIVGLQPEEGSSIPGIRRWP-------TEYLPGIFNASLVDEVLD 231

Query: 246 VSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMS 303
           +   D+ +  R LA  E +  G S G AV  AL+VA +A PDA++V ++ D G  Y+S
Sbjct: 232 IHQRDAENTMRELAVREGIFCGVSSGGAVAGALRVA-KANPDAVVVAIICDRGDRYLS 288


Lambda     K      H
   0.316    0.135    0.398 

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: 407
Number of extensions: 18
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: 464
Length of database: 303
Length adjustment: 30
Effective length of query: 434
Effective length of database: 273
Effective search space:   118482
Effective search space used:   118482
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