GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Burkholderia phytofirmans PsJN

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BPHYT_RS03225 BPHYT_RS03225 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS03225 BPHYT_RS03225
           3-hydroxyacyl-CoA dehydrogenase
          Length = 811

 Score = 1266 bits (3275), Expect = 0.0
 Identities = 640/811 (78%), Positives = 709/811 (87%), Gaps = 4/811 (0%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MSN I++KVAVLGAGVMGAQIAAHLINA+VPV+LFDLPAKEGPKN IAL+AIENLKKLSP
Sbjct: 1   MSNLIIRKVAVLGAGVMGAQIAAHLINAKVPVLLFDLPAKEGPKNAIALKAIENLKKLSP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           AP G+K++A  IQ ANY+DDI  L ECDLVIEAIAERMDWKHDLYKKVAPHLA +AIFAT
Sbjct: 61  APFGVKDDAQYIQPANYDDDIEKLAECDLVIEAIAERMDWKHDLYKKVAPHLAPNAIFAT 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSITALS+GF  +LK+RFCGVHFFNPPRYMHLVELIPTATT+P+ILDQLE+FLT+ 
Sbjct: 121 NTSGLSITALSEGFSDELKARFCGVHFFNPPRYMHLVELIPTATTRPEILDQLESFLTSV 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           +GKGVVRAKDTPNFIANRVGIFSILAV  EA KFG+ FD VDDLTG++LGRAKSATFRTA
Sbjct: 181 VGKGVVRAKDTPNFIANRVGIFSILAVVTEAAKFGLRFDEVDDLTGARLGRAKSATFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDTMAHVIKTMQDTL DDPF PVY+TPAVL  LV  GALGQKTG GFYKKEGKAIK
Sbjct: 241 DVVGLDTMAHVIKTMQDTLKDDPFFPVYETPAVLAELVKKGALGQKTGGGFYKKEGKAIK 300

Query: 301 VLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360
           VLD KTG+YVD G  ADE+V R+LK+  AER+KLLRES +PQAQFLWA+FRDV+HYI V+
Sbjct: 301 VLDPKTGEYVDGGANADELVGRILKRPPAERLKLLRESEHPQAQFLWAIFRDVYHYIGVH 360

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

Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480
            EGPVAE  GVH   GSWSPA+++FV RS L VY +Q FRA + G   ADP+  G+T+ E
Sbjct: 421 LEGPVAEQGGVHTNEGSWSPASKTFVPRSSLSVYDKQVFRAPLVGETKADPKTYGKTLFE 480

Query: 481 NDAVRIWVSE--GQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538
            DAVR WV +  G++DVL+VSFKSKMNTIGP VIDGLT+AI+LAE  YKGLVVWQPTSL+
Sbjct: 481 TDAVRAWVDDRAGENDVLIVSFKSKMNTIGPSVIDGLTQAIELAEKDYKGLVVWQPTSLK 540

Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598
           LG PGGPFSAGANLE AMPAFMMGGAKGIEPFVK+FQ GM+RVKYASVPV+SA SGIALG
Sbjct: 541 LGTPGGPFSAGANLEEAMPAFMMGGAKGIEPFVKKFQQGMLRVKYASVPVISAVSGIALG 600

Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTN-ILQFL 657
           GGCEL LHSA RVA +E+Y GLVEVGVGLVPAGGGLKEAAL AA AA   G+TN +L+F+
Sbjct: 601 GGCELALHSAKRVAHIESYFGLVEVGVGLVPAGGGLKEAALRAAEAATQVGATNDLLKFV 660

Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPL-P 716
              F++AAMAKVSASAL+AR MGYL+PSD IVFNV ELL VA+ E RAL+SAGYR PL  
Sbjct: 661 QKSFENAAMAKVSASALDARAMGYLKPSDTIVFNVFELLDVAKKEARALSSAGYRPPLRV 720

Query: 717 TLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLA 776
           T VPVAGRS IATIKASLVNMRDG FIS HDFLIASRIAEAVCGGDVEAGSLV E+WLL 
Sbjct: 721 TQVPVAGRSAIATIKASLVNMRDGRFISEHDFLIASRIAEAVCGGDVEAGSLVDEEWLLQ 780

Query: 777 LERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           LER+AFVDLLGT KTQERIMGMLQTGKPVRN
Sbjct: 781 LERRAFVDLLGTQKTQERIMGMLQTGKPVRN 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: 1773
Number of extensions: 67
Number of successful extensions: 5
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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