Alignments for a candidate for fadB in Cupriavidus basilensis 4G11

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.

Downloads

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, 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

GapMind for catabolism of small carbon sources