GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Marinobacter adhaerens HP15

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF2651 HP15_2595 acyl-CoA synthetase

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__Marino:GFF2651
          Length = 547

 Score =  270 bits (689), Expect = 1e-76
 Identities = 173/536 (32%), Positives = 273/536 (50%), Gaps = 21/536 (3%)

Query: 19  YSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFI 78
           Y +L   L L    +Y  D+  V    S+YTY+   + +   A+AL   G    D ++ +
Sbjct: 16  YPLLIKRLLLS-GPRYNPDQEIVYSNRSKYTYTDLVERIHRLANALTDAGVKPGDTVAVM 74

Query: 79  SRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKD 138
             + P +LE FF +P  G +L  +N RLSP ++ Y +NH++   V+V + +L  +  VKD
Sbjct: 75  DWDTPRYLECFFAIPMIGAILHTVNIRLSPDQIVYTMNHAEDDVVLVHDDFLPIIEAVKD 134

Query: 139 QIKA--EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTS 196
           +IK     I L D DN   ++ A  E    Y +L+   + D    P  +E S+ T +YT+
Sbjct: 135 EIKTVKTWIQLTDSDN---AQQAPVEAVGEYEDLL-ARANDKFDFPDFDENSVATTFYTT 190

Query: 197 GTTGLPKGVMHHHRGAFLNAMAEVLE----HQMDL---NSVYLWTLPMFHAASWGFSWAT 249
           GTTG PKGV   HR   L+ +A         +M L   +SVY+   PMFH  +WG  +A 
Sbjct: 191 GTTGNPKGVYFSHRQLVLHTLAMTGTVASFDEMPLMRSSSVYMPVTPMFHVHAWGVPYAA 250

Query: 250 VAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309
             +G   V   + +  L+  L+++ +VT     PT+   +           SN  H+L+ 
Sbjct: 251 TMMGIKQVYPGRYEPELLVDLLKEHKVTFSHCVPTIMQMMMATESIKTADLSNW-HVLIG 309

Query: 310 GAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY 369
           G+A       A  ++G  +   YG++ET         + E   LPLE+Q  ++ + GI  
Sbjct: 310 GSALTKGLCDAGAKLGIKLYTAYGMSETCPLLCASHLKPEDLELPLEQQTAIRVKTGIAT 369

Query: 370 VSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVV 429
              E+++ D  G PVP DG+  GE+V R   +  GY+K PEK  + +  GW H+GD A +
Sbjct: 370 PMVELEIVDPEGNPVPHDGEAKGEIVARAPWLTQGYFKEPEKGEQLWEGGWLHTGDVASM 429

Query: 430 HPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIE 489
            PD  I I DR KD+I TGGE +SS+ +E  + +   V   AV G PDEKWGE   A + 
Sbjct: 430 EPDNTITIKDRIKDVIKTGGEWLSSLDLENLISQHSAVAGAAVVGVPDEKWGERPHALVT 489

Query: 490 LQEGVKLTEEEVIKFCKE-----RLAHFECPKIVEF-GPIPMTATGKMQKYVLRNE 539
           L+ G + + E++    K+      +  +  P+ ++F   IP T+ GK+ K ++R++
Sbjct: 490 LKPGEQASAEDIQNHLKQFVESGEINKWAIPEHIDFVEDIPKTSVGKINKKLIRDQ 545


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: 745
Number of extensions: 37
Number of successful extensions: 6
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: 547
Length adjustment: 36
Effective length of query: 513
Effective length of database: 511
Effective search space:   262143
Effective search space used:   262143
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