GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Cupriavidus basilensis 4G11

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate RR42_RS25360 RR42_RS25360 acyl-CoA synthetase

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__Cup4G11:RR42_RS25360
          Length = 554

 Score =  376 bits (966), Expect = e-108
 Identities = 212/530 (40%), Positives = 300/530 (56%), Gaps = 5/530 (0%)

Query: 11  GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70
           G+D   + +  LTPL FL+R  + + D+TA+++   R ++    +     ASAL++RG  
Sbjct: 9   GLDRRAANHMPLTPLHFLDRCAEQYPDRTAIIHGPVRQSWKVTRERCRQLASALVKRGVG 68

Query: 71  REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYL 130
           R D +S ++ N P  +E+  G+P +G VL  IN RL    + +I+ H + K + VD  + 
Sbjct: 69  RGDTVSILAPNTPAMVEAHHGIPLSGAVLNAINCRLDADGVRFIVAHGECKVLFVDREFS 128

Query: 131 NSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMI 190
               E    +    ++++  D  + +        M Y + ++ G  D   +   +E++ I
Sbjct: 129 ALAAEALQGLPNAPLVIDIAD--ALAPAGEPIGAMEYEQFLREGDIDFPGVWPDDEWNAI 186

Query: 191 TLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATV 250
            L YTSGTT  PKGV+  HRGA+L +M ++ +  M     YLWTLPMFHA  W FSWA  
Sbjct: 187 ALNYTSGTTSDPKGVVPSHRGAYLMSMLQLTDWGMPRAPKYLWTLPMFHANGWCFSWAVT 246

Query: 251 AVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAG 310
           A   T+VCL KV    I+  +E     H CAAP V  +LA   +     FS+ V +  AG
Sbjct: 247 AAAGTHVCLRKVTAANIFSAIEAYGADHFCAAPIVLSSLATATQEERRPFSHVVRIRTAG 306

Query: 311 AAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYV 370
           + P  + LKA+ E G  + HVYG+TE  G          W+    +E+A+L ARQG    
Sbjct: 307 SPPPASVLKAVIEQGFDVEHVYGITEASGTPVSSYANPAWNEKSGDEKARLMARQGNRAA 366

Query: 371 SFE-MDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAV 428
             E + V D +  + VPWDG T GE+++RG+ V  GY KNPE T  +F  GWFH+GD AV
Sbjct: 367 GLEGLRVADPDTMESVPWDGTTQGELLLRGNIVMKGYLKNPEATEAAFAGGWFHTGDLAV 426

Query: 429 VHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARI 488
           VHPDGY++I DR KD+I +GGE +SS+ VE  L + P V   AV   P  KWGE   A I
Sbjct: 427 VHPDGYVQITDRSKDVIISGGENISSVEVEDVLHQHPAVLIAAVVAQPHPKWGESPCAFI 486

Query: 489 ELQEGVKL-TEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLR 537
           EL+ GV   TE E+I FC+ RLAH++CP  V +G +P T TGK+QKY LR
Sbjct: 487 ELKNGVAAPTEAEIIAFCRSRLAHYKCPTRVVYGALPKTGTGKIQKYRLR 536


Lambda     K      H
   0.319    0.136    0.411 

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: 735
Number of extensions: 29
Number of successful extensions: 5
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: 549
Length of database: 554
Length adjustment: 36
Effective length of query: 513
Effective length of database: 518
Effective search space:   265734
Effective search space used:   265734
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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