GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CBS in Pseudomonas fluorescens FW300-N2C3

Align Putative cystathionine beta-synthase MT1108; EC 4.2.1.22; Beta-thionase; Serine sulfhydrase (uncharacterized)
to candidate AO356_19050 AO356_19050 cysteine synthase

Query= curated2:P9WP50
         (464 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_19050
          Length = 300

 Score =  210 bits (535), Expect = 4e-59
 Identities = 123/305 (40%), Positives = 178/305 (58%), Gaps = 16/305 (5%)

Query: 7   ISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGT 66
           I++ +G TPLVRL  +  +   T+  K+E  NP GS KDR A+ MI   E  GQ++PG T
Sbjct: 8   IADCVGNTPLVRLQRLPGETTNTLLLKLEGNNPAGSVKDRPALSMITRGELRGQIQPGDT 67

Query: 67  IVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPA 126
           ++E TSGNTG+ LA+ A  +GYK + + PD  S +++  + AYGAE+++           
Sbjct: 68  LIEATSGNTGIALAMAAAIKGYKMILIMPDNSSAERKAAMTAYGAELIL---VTQEQGME 124

Query: 127 SYYSVSDRLVRDIDGAWKP-DQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGT 185
               +++R+    +G  K  DQ+AN + P +HY TTGPEIW  T+G +THFV+ +GT GT
Sbjct: 125 GARDLAERM--QAEGRGKVLDQFANGDNPEAHYTTTGPEIWRQTDGTITHFVSSMGTTGT 182

Query: 186 ITGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEII 244
           I G  RYLKE     V+I+G  P EGS   G    P       E++ P  Y     D II
Sbjct: 183 IMGTSRYLKE-QNPNVQIIGLQPMEGSAIPGIRRWP-------EEYLPKIYQADRVDRII 234

Query: 245 AVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMSK 304
            ++ S++ D+TRRLAREE +  G S G AV   L++++E   +A+IV ++ D G  Y+S 
Sbjct: 235 DMAQSEAEDVTRRLAREEGIFCGVSSGGAVAGMLRLSKEV-ENAVIVAIICDRGDRYLST 293

Query: 305 IFNDA 309
              DA
Sbjct: 294 GIFDA 298


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: 374
Number of extensions: 14
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: 300
Length adjustment: 30
Effective length of query: 434
Effective length of database: 270
Effective search space:   117180
Effective search space used:   117180
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: 49 (23.5 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