GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Burkholderia phytofirmans PsJN

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate BPHYT_RS33490 BPHYT_RS33490 acyl-CoA synthetase

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__BFirm:BPHYT_RS33490
          Length = 543

 Score =  405 bits (1041), Expect = e-117
 Identities = 224/542 (41%), Positives = 321/542 (59%), Gaps = 18/542 (3%)

Query: 11  GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70
           G++   + Y  LTP+ F+ RA + + ++ AVV+ + R  +   Y+     ASAL + G  
Sbjct: 8   GLERREANYVPLTPIDFIVRAAEVYGERPAVVHGEIRRNWRETYERARRLASALQQAGIQ 67

Query: 71  REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY- 129
           R D ++ +  N P  +E+ FGVP AG VL  +N RL    + +++ H ++K ++VD  Y 
Sbjct: 68  RGDTVAALLPNIPPMIEAHFGVPMAGAVLNTLNTRLDVSSLLFMLRHGEAKALIVDTEYG 127

Query: 130 ---LNSLLEVKDQIKAEIILLED--PDNPSASETARKEVRMT-YRELVKGGSRDPLPIPA 183
                + LE  D     +I + D  P +PS      + +R T Y   ++ G  +      
Sbjct: 128 EFAHRAALEFPD---LRVISVADAMPADPS------QFIRATDYEAFLQSGDPEFAWAMP 178

Query: 184 KEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASW 243
            +E+  I L YTSGTTG PKGV++HHRGA+LNA++ +LE  M  +++YLWTLP+FH   W
Sbjct: 179 ADEWDAIALNYTSGTTGDPKGVVYHHRGAYLNALSNILEWDMPKHAIYLWTLPLFHCNGW 238

Query: 244 GFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNR 303
            F W   A    NVCL K D   ++ L+ +E +TH C AP V   LA+   +      +R
Sbjct: 239 CFPWTVAARAGVNVCLRKFDAKTVFDLIRREGITHYCGAPIVQSALANAPAQWREGIEHR 298

Query: 304 VHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKA 363
           V  +VAGAAPAPA +  M+EIG  + HVYGLTETYGP ++C  + EW++L    +A++ A
Sbjct: 299 VSTMVAGAAPAPAVIAKMKEIGFDLTHVYGLTETYGPAAVCAKQEEWEALDDGARAEMNA 358

Query: 364 RQGIPY-VSFEMDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWF 421
           RQG+ Y +   + V D +   PVP DG+TIGE++ RG+    GY KN   T  +F+ GWF
Sbjct: 359 RQGVRYHLQAAVTVLDPDTLTPVPDDGETIGEIMFRGNICMKGYLKNERATEATFQGGWF 418

Query: 422 HSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWG 481
           H+GD  V  PDGYI I DR KD+I +GGE +SSI VE TL   P V   AV    D KWG
Sbjct: 419 HTGDLGVRMPDGYIRIRDRSKDIIISGGENISSIEVEDTLYRHPAVSVAAVVAMADPKWG 478

Query: 482 EVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541
           EV  A +EL+EG +++ EE+I  C+  LA ++ PK V FG +P T+TGK+QK+ LR   K
Sbjct: 479 EVPCAFVELKEGAQVSAEEIIAHCRLFLAGYKLPKAVRFGELPKTSTGKIQKFELRARIK 538

Query: 542 AK 543
           A+
Sbjct: 539 AE 540


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: 777
Number of extensions: 29
Number of successful extensions: 3
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: 543
Length adjustment: 35
Effective length of query: 514
Effective length of database: 508
Effective search space:   261112
Effective search space used:   261112
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 17 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