GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4889
          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:

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