Alignments for a candidate for ech in Burkholderia vietnamiensis G4

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Burkholderia vietnamiensis G4

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011885989.1 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000016205.1:WP_011885989.1
          Length = 811

 Score = 1250 bits (3234), Expect = 0.0
 Identities = 628/811 (77%), Positives = 709/811 (87%), Gaps = 4/811 (0%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MSNF+++KVAVLGAGVMGAQIAAHL+NARVPV+LFDLPAKEGPKN IAL+AIENLKKLSP
Sbjct: 1   MSNFLIRKVAVLGAGVMGAQIAAHLVNARVPVLLFDLPAKEGPKNAIALKAIENLKKLSP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           AP G+K++A  ++AANYEDDIA L ECD+VIEAIAERMDWKHDLYKKVAPH+A +AIFAT
Sbjct: 61  APFGVKDDAKYLEAANYEDDIAKLAECDVVIEAIAERMDWKHDLYKKVAPHIAPNAIFAT 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSIT LS+GF  +LK+RFCGVHFFNPPRYMHLVELIPTA T+P+ILDQLE FLT+ 
Sbjct: 121 NTSGLSITKLSEGFSDELKARFCGVHFFNPPRYMHLVELIPTAHTRPEILDQLETFLTSV 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           +GKGVVRAKDTPNFIANRVGIFSILAV AEA KFG+ FD VDDLTG++LGRAKSATFRTA
Sbjct: 181 VGKGVVRAKDTPNFIANRVGIFSILAVIAEAAKFGLRFDEVDDLTGARLGRAKSATFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDTMAHVI+TMQD L DDPF PVY+TPAVL  LV  GALGQKTG GFYKKEGKAIK
Sbjct: 241 DVVGLDTMAHVIRTMQDNLADDPFFPVYETPAVLAELVKQGALGQKTGGGFYKKEGKAIK 300

Query: 301 VLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360
           VLDAKTG YVD+G KADE V R+LK+  AER+KLLRE+ +P AQFLW++FRDVFHYI V+
Sbjct: 301 VLDAKTGAYVDSGAKADETVGRILKRPPAERLKLLRETDHPHAQFLWSIFRDVFHYIGVH 360

Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420
           LE IA +A D+DLAIRWGFGWN GPFE WQ+AGWKQVAEWV+ED+ AGKAL+  PLP+WV
Sbjct: 361 LESIADNARDVDLAIRWGFGWNEGPFEGWQAAGWKQVAEWVQEDIAAGKALANVPLPSWV 420

Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480
            EGPVAE  GVH A GSW+PA++ FV RS L VY +Q FRA + G A ADP+  G+T+ E
Sbjct: 421 LEGPVAEKGGVHTAEGSWAPASKRFVPRSDLAVYGKQVFRAPLLGEAGADPKTYGKTLFE 480

Query: 481 NDAVRIWVSE--GQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538
            DAVR WV +  G+DDV++VSFKSKMNTIGP VIDGL +AI+LAE  YKG+V+WQPTSL+
Sbjct: 481 TDAVRAWVDDRAGEDDVVIVSFKSKMNTIGPSVIDGLVQAIELAEQDYKGVVIWQPTSLK 540

Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598
           LG PGGPFSAGANLE AMPAFMMGGAKGIEPFVK+FQ+GM+RVKYA+VPVV+A SGIALG
Sbjct: 541 LGTPGGPFSAGANLEEAMPAFMMGGAKGIEPFVKKFQEGMLRVKYANVPVVAAVSGIALG 600

Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAA-GSTNILQFL 657
           GGCELMLHSA RV  +E+YIGLVEVGVGLVPAGGGLKEAAL AA AA AA  +T+IL+F+
Sbjct: 601 GGCELMLHSAKRVVHVESYIGLVEVGVGLVPAGGGLKEAALRAADAATAANATTDILKFV 660

Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT 717
           T  F++AAMAKVS+SA +AR MGY++PSD IVFNV ELL  A+ E RALA+ GYRAPL  
Sbjct: 661 TKSFENAAMAKVSSSAHDARAMGYVKPSDTIVFNVFELLDTAKKEARALAATGYRAPLRA 720

Query: 718 L-VPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLA 776
             VPVAGRS IATIKASLVNMRDG FIS HDFLIASRIAE VCGGDVEAGS+V E WLLA
Sbjct: 721 KDVPVAGRSAIATIKASLVNMRDGRFISDHDFLIASRIAEVVCGGDVEAGSVVDEQWLLA 780

Query: 777 LERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           LER+AFV+LLGT KTQERIMGMLQTGKPVRN
Sbjct: 781 LERRAFVELLGTQKTQERIMGMLQTGKPVRN 811


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: 1768
Number of extensions: 69
Number of successful extensions: 4
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: 811
Length adjustment: 41
Effective length of query: 766
Effective length of database: 770
Effective search space:   589820
Effective search space used:   589820
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