GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Cupriavidus basilensis 4G11

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate RR42_RS02510 RR42_RS02510 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>FitnessBrowser__Cup4G11:RR42_RS02510
          Length = 808

 Score = 1485 bits (3844), Expect = 0.0
 Identities = 751/808 (92%), Positives = 780/808 (96%), Gaps = 1/808 (0%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MSNFIVKKVAVLGAGVMGAQIAAHL+NARVPVVLFDLPAKEGPKNGI+LRAIENLKKLSP
Sbjct: 1   MSNFIVKKVAVLGAGVMGAQIAAHLVNARVPVVLFDLPAKEGPKNGISLRAIENLKKLSP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           APLGI +EAGLIQAANYEDD+ALLKECD+VIEAIAERMDWKHDLYKKVAPHLASH IFAT
Sbjct: 61  APLGINDEAGLIQAANYEDDLALLKECDVVIEAIAERMDWKHDLYKKVAPHLASHTIFAT 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQP ILD+LE FLT+T
Sbjct: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPAILDRLETFLTST 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEK+GIPFDVVDDLTGSKLGRAKSATFRTA
Sbjct: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKYGIPFDVVDDLTGSKLGRAKSATFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDTMAHVIKTMQDTL DDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK
Sbjct: 241 DVVGLDTMAHVIKTMQDTLMDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300

Query: 301 VLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360
           VLD KTGQYVD+GKKADEIVVRMLKK+ AERIKLLRESTNPQAQFLWAVFRDVFHYI VY
Sbjct: 301 VLDPKTGQYVDSGKKADEIVVRMLKKEPAERIKLLRESTNPQAQFLWAVFRDVFHYIGVY 360

Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420
           LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKED+EAGK L+   LPAWV
Sbjct: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDIEAGKGLANVALPAWV 420

Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480
           F GPVAENQGVH A GSWSPA Q+FV R+ LPVY RQ FRAA+KGTAAADPRKAGRTVEE
Sbjct: 421 FAGPVAENQGVHGAQGSWSPAAQAFVQRNALPVYARQVFRAALKGTAAADPRKAGRTVEE 480

Query: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLG 540
           NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDV DGLTRAIDLA+A YKGLVVWQPTSLQLG
Sbjct: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVTDGLTRAIDLAQAEYKGLVVWQPTSLQLG 540

Query: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGG 600
           APGGPFSAGANLEAAMPAFMMGGAKGIEPFVK+FQDGMMRVKY++VPVVSAASGIALGGG
Sbjct: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKKFQDGMMRVKYSAVPVVSAASGIALGGG 600

Query: 601 CELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSR 660
           CELMLHSA RVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTN LQFLT+R
Sbjct: 601 CELMLHSAKRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNYLQFLTNR 660

Query: 661 FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLP-TLV 719
           FQ+AAMAKVSASAL+A++MGYLQPSD IVFNVHELL+VAQNEVRAL++AGYRAP+P TLV
Sbjct: 661 FQAAAMAKVSASALDAQKMGYLQPSDTIVFNVHELLHVAQNEVRALSNAGYRAPVPGTLV 720

Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779
           PVAGRSGIATIKASL NMRDGGFIS HDFLIASRIAEAVCGGDVEAGSLVSE+WLLALER
Sbjct: 721 PVAGRSGIATIKASLANMRDGGFISAHDFLIASRIAEAVCGGDVEAGSLVSEEWLLALER 780

Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           KAFVDLLGTGKTQERIMGMLQTGKPVRN
Sbjct: 781 KAFVDLLGTGKTQERIMGMLQTGKPVRN 808


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: 1995
Number of extensions: 76
Number of successful extensions: 2
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: 808
Length adjustment: 41
Effective length of query: 766
Effective length of database: 767
Effective search space:   587522
Effective search space used:   587522
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