GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Dokdonella koreensis DS-123

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_067645581.1 I596_RS06330 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_001632775.1:WP_067645581.1
          Length = 790

 Score =  879 bits (2272), Expect = 0.0
 Identities = 462/808 (57%), Positives = 569/808 (70%), Gaps = 23/808 (2%)

Query: 2   SNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPA 61
           +  +++K AVLGAGVMGAQIAAHL+NA +  +LFDLPAKEG KNGI  +AI NL KLSPA
Sbjct: 4   NTLLIRKAAVLGAGVMGAQIAAHLVNAGIETILFDLPAKEGDKNGIVTQAIANLAKLSPA 63

Query: 62  PLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATN 121
           PL  K  A  I  ANY++D+  L ECDLVIEAIAERMDWK DLY+++APHL+  A  A+N
Sbjct: 64  PLAEKSLAAAIVPANYDEDLGRLGECDLVIEAIAERMDWKLDLYRRIAPHLSDSAFVASN 123

Query: 122 TSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTL 181
           TSGLSI  L+D   A L+ RF G+HFFNPPRYMHLVE+IP   T P +L  LEAFLTT L
Sbjct: 124 TSGLSINTLADALPAALRRRFSGIHFFNPPRYMHLVEVIPARETDPALLAGLEAFLTTQL 183

Query: 182 GKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTAD 241
           GKGVV A+DTPNFI NR+G+FSILA     E+FG+ FD VD +TG  +GR KSAT+RT+D
Sbjct: 184 GKGVVYARDTPNFIGNRIGVFSILATMHHTEQFGLGFDEVDAITGPAIGRPKSATYRTSD 243

Query: 242 VVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKV 301
           VVGLDTMAHVIKTM DTL +DP+   +K PA L+ L+D GALGQKTGAGF++K GK I V
Sbjct: 244 VVGLDTMAHVIKTMADTLPEDPWHAYFKAPAWLQALIDQGALGQKTGAGFFRKVGKDIHV 303

Query: 302 LDAKTGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360
           LD     Y  AG+ A E V  +L  +D AE+   LR ST+ QAQFLWA+FRD+FHY A +
Sbjct: 304 LDLAQRDYRPAGRAASEEVAAILAIRDPAEKFAKLRASTDRQAQFLWAMFRDLFHYSAYH 363

Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420
           L  +A +A ++DLAIRWG+GW  GPFE WQ+AGW+QVA+W+ ED+ AGKA+S+APLPAWV
Sbjct: 364 LADLAETAREVDLAIRWGYGWKLGPFETWQAAGWRQVAQWINEDIAAGKAMSSAPLPAWV 423

Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480
            +G     +GVH A G++S +    + RS  PVY+RQ F   + G    +    G T  E
Sbjct: 424 TDG----REGVHVAEGAYSASAGRPLPRSAHPVYRRQRFPDPLLG----ERFDTGTTAWE 475

Query: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLG 540
           N+ VR+W     D+V +VSFK+KMNT+   V+DG+ RAID AE  +KG+V+WQ       
Sbjct: 476 NEGVRLW--HLGDEVGIVSFKTKMNTVNDAVLDGIQRAIDEAEKTFKGVVLWQ------- 526

Query: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGG 600
             G PFSAGA+L+ A+     G     +  V  FQ    R+KYA VPVV+A  G+A GGG
Sbjct: 527 -TGEPFSAGADLKGALGLLQAGKVDAFDAMVANFQATSQRIKYALVPVVAAVRGMAFGGG 585

Query: 601 CELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSR 660
           CE  +HSA  VAALE+YIGLVE GVGL+PAGGGLKE AL   RAA  AG  +    +   
Sbjct: 586 CEFQMHSARTVAALESYIGLVEAGVGLLPAGGGLKEIAL---RAATQAGGGDPFDGVKRM 642

Query: 661 FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT-LV 719
           F++ AMAKVS SALEA+Q+G L+P D +VFN +ELL+VA     ALA  GYR PLP   +
Sbjct: 643 FETIAMAKVSGSALEAKQLGLLRPDDVVVFNAYELLHVASTVAGALAEQGYRPPLPARAI 702

Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779
           PVAG  G AT+K  LVNM +G FIS HDF +ASRIA+ +CGG +E GS V E WLL LER
Sbjct: 703 PVAGDVGTATLKMLLVNMLEGRFISPHDFDVASRIADTLCGGSIERGSQVDERWLLDLER 762

Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           + FV+L  T KTQERI   L TGKP+RN
Sbjct: 763 RHFVELAQTAKTQERIAHTLATGKPLRN 790


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: 1633
Number of extensions: 69
Number of successful extensions: 8
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: 790
Length adjustment: 41
Effective length of query: 766
Effective length of database: 749
Effective search space:   573734
Effective search space used:   573734
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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