Alignments for a candidate for ech in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Paraburkholderia phymatum STM815

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_012399805.1 BPHY_RS01920 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000020045.1:WP_012399805.1
          Length = 814

 Score = 1241 bits (3212), Expect = 0.0
 Identities = 628/814 (77%), Positives = 704/814 (86%), Gaps = 7/814 (0%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MSN I++KVAVLGAGVMGAQIAAHLINA+VPV+LFDLPAKEGPKNGIAL+AIENLKKLSP
Sbjct: 1   MSNLIIRKVAVLGAGVMGAQIAAHLINAKVPVLLFDLPAKEGPKNGIALKAIENLKKLSP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           AP G K++A  IQ ANY+DDI  L ECD+VIEAIAERMDWKHDLYKKV+PH+ ++AIFAT
Sbjct: 61  APFGAKDDAQYIQPANYDDDIEKLAECDVVIEAIAERMDWKHDLYKKVSPHIGANAIFAT 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSIT LS GF  +LK+RFCGVHFFNPPRYMHLVELIPTATT+P+ILDQLE FLT+ 
Sbjct: 121 NTSGLSITELSKGFSDELKARFCGVHFFNPPRYMHLVELIPTATTRPEILDQLETFLTSV 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           +GKGVVRAKDTPNFIANRVGIFSILAV  EAEKFG+ FD VDDLTGS+LGRAKSATFRTA
Sbjct: 181 VGKGVVRAKDTPNFIANRVGIFSILAVIKEAEKFGLRFDEVDDLTGSRLGRAKSATFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDTMAHVIKTMQD L DDPF  VY+TPAVL GLV  GALGQKTGAGFYKKEGKAIK
Sbjct: 241 DVVGLDTMAHVIKTMQDNLADDPFFAVYETPAVLTGLVQQGALGQKTGAGFYKKEGKAIK 300

Query: 301 VLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360
           VLDAK+G YVD G KADE+V R+LK+  AER+KLLRES +PQAQFLWA+FRDVFHYI V+
Sbjct: 301 VLDAKSGSYVDGGAKADELVGRILKRPPAERLKLLRESQHPQAQFLWAIFRDVFHYIGVH 360

Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420
           LE IA +A D+D AIRWGFGW+ GPFE WQ+AGWKQ+A WV+ED+ AGKALS APLPAWV
Sbjct: 361 LESIADNARDVDFAIRWGFGWSEGPFEGWQTAGWKQIAGWVQEDIAAGKALSNAPLPAWV 420

Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTA---AADPRKAGRT 477
            EG VAE  GVH   GSWSPA + FV RS L VY RQ FRA + G +    ADP++ G+T
Sbjct: 421 LEGAVAEKGGVHTDEGSWSPAEKRFVPRSSLSVYDRQVFRAPLAGESNGGGADPKRYGKT 480

Query: 478 VEENDAVRIWVSE--GQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPT 535
           V E DAVR WV +  G++DVL+VSFKSKMNTIGP VIDG+ +AID AE  YK +V+WQP 
Sbjct: 481 VFETDAVRAWVDDRAGENDVLIVSFKSKMNTIGPSVIDGIEKAIDAAEKDYKAVVIWQPA 540

Query: 536 SLQLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGI 595
           SL+LGAPGGPFSAGANLE AMPAFMMGGAKGIEPFVK+FQ GM+RVKY++VPVV+A SGI
Sbjct: 541 SLKLGAPGGPFSAGANLEEAMPAFMMGGAKGIEPFVKKFQQGMLRVKYSNVPVVAAVSGI 600

Query: 596 ALGGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGST-NIL 654
           ALGGGCEL+LHSA RVA +E+YIGLVEVGVGLVPAGGGLKEAAL AA  A   G+T ++L
Sbjct: 601 ALGGGCELLLHSAKRVAHIESYIGLVEVGVGLVPAGGGLKEAALRAAETATQVGATSDLL 660

Query: 655 QFLTSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAP 714
           +FL   F++AAMAKVS SAL+AR MGYL+PSD IVFNV ELL  A+ E RALA+AGYRAP
Sbjct: 661 KFLQKSFENAAMAKVSTSALDARAMGYLKPSDTIVFNVFELLDTAKKEARALAAAGYRAP 720

Query: 715 L-PTLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDW 773
           L  T VPVAGRS ++TIKASLVNMRDG FIS HD+LIASRIAEAVCGGDVEAGSLV E+W
Sbjct: 721 LRVTQVPVAGRSAMSTIKASLVNMRDGRFISDHDYLIASRIAEAVCGGDVEAGSLVDEEW 780

Query: 774 LLALERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           LLALER+AFV+LLGT KTQERIMGMLQTGKPVRN
Sbjct: 781 LLALERRAFVELLGTQKTQERIMGMLQTGKPVRN 814


Lambda     K      H
   0.319    0.134    0.391 

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: 1767
Number of extensions: 69
Number of successful extensions: 6
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: 807
Length of database: 814
Length adjustment: 41
Effective length of query: 766
Effective length of database: 773
Effective search space:   592118
Effective search space used:   592118
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 (21.8 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 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