GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS33490 BPHYT_RS33490 acyl-CoA
           synthetase
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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