GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Herbaspirillum seropedicae SmR1

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate HSERO_RS23535 HSERO_RS23535 acyl-CoA synthetase

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__HerbieS:HSERO_RS23535
          Length = 546

 Score =  389 bits (1000), Expect = e-112
 Identities = 211/536 (39%), Positives = 312/536 (58%), Gaps = 6/536 (1%)

Query: 11  GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70
           G+    + Y+ LTP+ F+ RA   +  +TA+++   R  +   Y      ASAL   G  
Sbjct: 7   GLGRNAANYAALTPIDFIARAAAVYGKRTAIIHGALRQDWDQTYRRTRRLASALQGLGVG 66

Query: 71  REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYL 130
           + D +S +  N P  +E+ FGVP AG VL  +N RL  + + +++ H ++K +++D  + 
Sbjct: 67  KNDTVSAMLPNTPAMVEAHFGVPMAGAVLNALNIRLDAESIVFMLRHGEAKVLLIDSEFA 126

Query: 131 NSLLEVKDQIKA-EIILLEDPDNPSASETARKEVRMTYRELVKGGSRD-PLPIPAKEEYS 188
               +++ Q+ A +I+ + D   P      R    + Y  L+ GG       +PA +E+ 
Sbjct: 127 ALAQQLRTQLPALKIVEVFDELGPPPVAGERFG-HLEYEALLAGGDEHFDWQMPA-DEWD 184

Query: 189 MITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWA 248
            I L YTSGTTG PKGV++HHRGA LNA++ +LE  +  + VYLWTLPMFH   W F W 
Sbjct: 185 AIALNYTSGTTGDPKGVVYHHRGAALNAVSNILEWDLPKHPVYLWTLPMFHCNGWCFPWT 244

Query: 249 TVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLV 308
             A    NVCL K +  L++ L+ +  +TH CAAP V+  LA+  +         V  +V
Sbjct: 245 VAARAGVNVCLRKFEPKLVFDLIAEHGITHYCAAPIVHAALANAPEGWRAGIRGPVKAMV 304

Query: 309 AGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIP 368
           AGA P  A L  M+ +   + HVYGLTE YGP ++C  + EW++L ++++A  K+RQG+ 
Sbjct: 305 AGAPPPAAVLAKMEAMQFELTHVYGLTEVYGPAAVCAEQDEWNTLSVDQRAVQKSRQGVR 364

Query: 369 Y-VSFEMDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDA 426
           Y +   + V   +   PV  DG+ IGE++ RG+    GY KN   T E+F  GWFH+GD 
Sbjct: 365 YHLQSGVTVLSPDTMAPVAADGEEIGEIMFRGNICMKGYLKNDRATHEAFAGGWFHTGDL 424

Query: 427 AVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTA 486
            V++ DGYI+I DR KD+I +GGE +SS+ VE  L   P V A AV   PDEKWGE   A
Sbjct: 425 GVMNADGYIKIKDRSKDIIISGGENISSVEVEDVLYRHPAVLAAAVVAQPDEKWGETPCA 484

Query: 487 RIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKA 542
            +EL+EG ++   E+ +FC+  LA F+ PK + FGP+P T+TGK+QK+ LR   K+
Sbjct: 485 FVELKEGAEVGAAELTEFCRSHLAGFKVPKAIYFGPLPKTSTGKIQKFELRKRMKS 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: 706
Number of extensions: 30
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: 546
Length adjustment: 36
Effective length of query: 513
Effective length of database: 510
Effective search space:   261630
Effective search space used:   261630
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 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