GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Sphingopyxis indica DS15

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_089215041.1 CHB69_RS05855 fatty acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_900188185.1:WP_089215041.1
          Length = 518

 Score =  200 bits (508), Expect = 1e-55
 Identities = 158/519 (30%), Positives = 251/519 (48%), Gaps = 33/519 (6%)

Query: 27  FLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFL 86
           FL    K   D+ A+   D   +Y+   +     ASAL+  G  R D++++I +N   + 
Sbjct: 13  FLTHWAKERPDRVAMREEDRVMSYAELEERTARVASALLAAGLERGDRIAWIGKNSDLYF 72

Query: 87  ESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEIIL 146
             FFG   AG V+ PI +RLSP E A+I+N + +K +V   P  ++    +DQ+  +  L
Sbjct: 73  TLFFGAARAGIVMAPIGWRLSPVEWAFIVNDTRAK-IVFTGPGFDA---AEDQLAGK--L 126

Query: 147 LEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVM 206
             DP    A            R ++ G  R     P+    +++ LY TSGTTG PKG +
Sbjct: 127 DHDPQIIGADAA---------RAMIDGARRVAFD-PSGPADAVLQLY-TSGTTGNPKGAV 175

Query: 207 HHHRGAFL----NAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCLDKV 262
             +   F     +A  ++   + + +   L  +P  H    G     +A G   + L + 
Sbjct: 176 LTNTNLFALRRNSADLDLPYTRWEDDEAVLVAMPCAHIGGTGLGIMALAAGLPGIILAEF 235

Query: 263 DYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATL--KA 320
           +   ++  VE   VT     P     L  + +  ++ +S R+  ++ GAAP P  L  + 
Sbjct: 236 NPDGVFDAVEHHGVTRFFIVPAALQMLLLHPRCASVDYS-RLKYILYGAAPIPLDLLRQC 294

Query: 321 MQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDAN 380
           ++  G      YG+TET G  +IC    E D  P   +    A + +P V  E+ +   +
Sbjct: 295 IKMFGAQFIQAYGMTETTG--TICMLPPE-DHDPEGNRRMRSAGKPLPGV--EIRILGPD 349

Query: 381 GKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFR-DGWFHSGDAAVVHPDGYIEIVD 439
           G+ VP     +GEVV R  N   GY+  P+ TA +    GW H+GDA  +  DGY+ I D
Sbjct: 350 GEEVPTG--EVGEVVTRSSNNMQGYWNLPDATARTMTAGGWIHTGDAGYMDEDGYLYIHD 407

Query: 440 RFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEE 499
           R KD+I +GGE V    VE  +   P V+ VAV G PD KWGE V A +  + G+ +  +
Sbjct: 408 RMKDMIISGGENVYPAEVESAIYGHPAVQEVAVIGIPDPKWGETVKAVVVPKAGMTVEPD 467

Query: 500 EVIKFCKERLAHFECPKIVE-FGPIPMTATGKMQKYVLR 537
           ++I + +ER+A F+ P+ V+    +P  A+GK+ +  LR
Sbjct: 468 DIIAWARERIAAFKAPRSVDVIEALPRNASGKILRKDLR 506


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: 696
Number of extensions: 28
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: 518
Length adjustment: 35
Effective length of query: 514
Effective length of database: 483
Effective search space:   248262
Effective search space used:   248262
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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