GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech 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)



>FitnessBrowser__BFirm:BPHYT_RS03225
          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 (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