Alignments for a candidate for prpE in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate H281DRAFT_05558 H281DRAFT_05558 fatty-acyl-CoA synthase

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__Burk376:H281DRAFT_05558
          Length = 550

 Score =  405 bits (1041), Expect = e-117
 Identities = 223/532 (41%), Positives = 309/532 (58%), Gaps = 4/532 (0%)

Query: 8   NYEGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRR 67
           N  G+ P  + +  LTP+ FL+RA K F D+TAVVY   R T+          ASAL R 
Sbjct: 7   NDPGLRPRAANFDALTPVTFLQRAEKVFPDRTAVVYGSHRETWREHAATCRRFASALARA 66

Query: 68  GFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDE 127
           G    D ++ +  N P  L + F VP AG VL  IN RL  + ++YI+ HS+++ ++VD 
Sbjct: 67  GIEYGDVVALLMTNTPPMLAAHFAVPMAGAVLNTINTRLDAENVSYILGHSEARLIIVDA 126

Query: 128 PYLNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEY 187
            +L        +++    L+   D  +A   A  +V   Y   +  G  +      +EE+
Sbjct: 127 EFLELARTAVARLQHPPRLVCFADEQAAF-AASSDVE-DYVSFLASGDENASFCKVEEEW 184

Query: 188 SMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSW 247
           + I + YTSGTTG PKGV++ HRGA+L+A++ ++   +   + YLWTLP+FH   W   W
Sbjct: 185 TPIAVNYTSGTTGRPKGVVYSHRGAYLSAVSSIISWGVPKAASYLWTLPLFHCNGWCMPW 244

Query: 248 ATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHML 307
                G  +VCL +VD   I +L+  ERVTH C AP V+  + D  ++ +L F+  V  L
Sbjct: 245 VLALQGGKSVCLRRVDGDKIVQLINDERVTHYCGAPIVHALIRDRAQQQDLVFNPAVSAL 304

Query: 308 VAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGI 367
           + GA P  + + AM  IG  + H+YGLTETYGP +ICE +  W  L   E+A  KARQG+
Sbjct: 305 IGGAPPPASLIAAMDAIGVQLTHIYGLTETYGPAAICEQQPAWAELGEAERADRKARQGV 364

Query: 368 PY-VSFEMDVFDANGK-PVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGD 425
            Y +   M V + N    V  DG  +GE+V RG+   +GY K+ E T  +F  GWF SGD
Sbjct: 365 NYALQAGMTVMNCNSSDEVSADGAMMGEIVFRGNMTMMGYLKDSESTDRAFDGGWFRSGD 424

Query: 426 AAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVT 485
            AV+ PDGY+ I DR KD+I +GGE +SS+ VE  L     V A AV   PDEKWGEV  
Sbjct: 425 LAVLEPDGYVRIKDRSKDIIISGGENISSVEVEDVLYRHETVAAAAVVAMPDEKWGEVPV 484

Query: 486 ARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLR 537
           A +EL+EG   +E+ +I  C+E+LAHF+CPK V F PIP TATGK+QK VLR
Sbjct: 485 AIVELREGSHASEDALIAHCREQLAHFKCPKRVIFHPIPKTATGKIQKNVLR 536


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: 731
Number of extensions: 33
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: 550
Length adjustment: 36
Effective length of query: 513
Effective length of database: 514
Effective search space:   263682
Effective search space used:   263682
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources