GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cysK in Pseudomonas fluorescens FW300-N1B4

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Pf1N1B4_4889 Cystathionine beta-synthase (EC 4.2.1.22)

Query= BRENDA::P37887
         (308 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4889 Cystathionine
           beta-synthase (EC 4.2.1.22)
          Length = 458

 Score =  223 bits (569), Expect = 5e-63
 Identities = 125/306 (40%), Positives = 190/306 (62%), Gaps = 14/306 (4%)

Query: 7   SITELIGNTPIVKLNRLADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGKLKAGN 66
           ++ ELIGNTP+V+++R  D     ++LKLE  NPG S+KDRIGLAMI+ AE++G+L+ G 
Sbjct: 8   AVLELIGNTPLVRISRF-DTGPCTLFLKLESQNPGGSIKDRIGLAMIDTAERDGRLRPGG 66

Query: 67  TIIEPTSGNTGIGLAMVAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAEGMKGA 126
           TI+E T+GNTG+GLA+V  AKG + +LV+PD MS E+   L+A GAE+ +T    G KG 
Sbjct: 67  TIVEATAGNTGLGLALVGRAKGYRVVLVVPDKMSTEKVLHLKAMGAEVHITRSDVG-KGH 125

Query: 127 IKKAEELAEKHGYFVP-----QQFNNPSNPEIHRQTTGKEIVEQFGDDQLDAFVAGIGTG 181
               +++A +    +P      QFNNP+NP  H  +T  EI  Q   D +DA V G+G+ 
Sbjct: 126 PDYYQDVAARLARDIPDAFFADQFNNPANPLAHECSTAPEIWAQTQHD-VDAIVVGVGSA 184

Query: 182 GTITGAGEVLKEAYPSIKIYAVEPSDSPVL----SG--GKPGPHKIQGIGAGFVPDILNT 235
           GT+TG     +   P++++   +P  S +     SG  G PG   ++GIG  F+P I + 
Sbjct: 185 GTLTGLTRFFQRVQPNLEMVLADPVGSVMAEYSRSGTLGTPGSWAVEGIGEDFIPSIADL 244

Query: 236 EVYDEIFPVKNEEAFEYARRAAREEGILGGISSGAAIYAALQVAKKLGKGKKVLAIIPSN 295
               + + + +EE+F++AR+  R EGILGG S+G  + AAL+  ++  + K+V++ +   
Sbjct: 245 SSVRKAYSISDEESFDHARQLLRAEGILGGSSTGTLLAAALRYCREQTEPKRVVSFVCDT 304

Query: 296 GERYLS 301
           G RYLS
Sbjct: 305 GTRYLS 310


Lambda     K      H
   0.313    0.134    0.373 

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: 294
Number of extensions: 14
Number of successful extensions: 4
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: 308
Length of database: 458
Length adjustment: 30
Effective length of query: 278
Effective length of database: 428
Effective search space:   118984
Effective search space used:   118984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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