GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Lysobacter daejeonensis GH1-9

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_036133695.1 N800_RS01000 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000768355.1:WP_036133695.1
          Length = 791

 Score =  886 bits (2289), Expect = 0.0
 Identities = 465/810 (57%), Positives = 567/810 (70%), Gaps = 22/810 (2%)

Query: 1   MSN-FIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLS 59
           MSN  +V++ AVLGAGVMGAQIAAHL NA V  VLFDLPAKEG  NG+  +AI NL KLS
Sbjct: 1   MSNKLLVRRAAVLGAGVMGAQIAAHLTNAGVDTVLFDLPAKEGDPNGVVTKAIANLVKLS 60

Query: 60  PAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFA 119
           PAPL  K  A  I  ANYE  + LLK CDL+IEAIAERMDWK DLYKK+AP + +H + A
Sbjct: 61  PAPLADKALAERIVPANYETGLELLKGCDLIIEAIAERMDWKQDLYKKIAPFVPAHTVLA 120

Query: 120 TNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTT 179
           +NTSGL I  L++    +++ RFCGVHFFNPPRYMHL ELIP  TT   +L+ LE FLTT
Sbjct: 121 SNTSGLGINKLAEVLPEEMRHRFCGVHFFNPPRYMHLAELIPARTTDASVLEGLETFLTT 180

Query: 180 TLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRT 239
           TLGKGVV AKDTPNFI NR+G+FS+LA     E+ G+ FD VD LTG  +GR KSAT+RT
Sbjct: 181 TLGKGVVIAKDTPNFIGNRIGVFSMLAAMHHTEQLGLGFDTVDALTGPAIGRPKSATYRT 240

Query: 240 ADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAI 299
           ADVVGLDTMAHVIKTM DTL +DP+   +K P  L  L++ GALGQKTGAG Y K GK I
Sbjct: 241 ADVVGLDTMAHVIKTMADTLPEDPWHAYFKAPKWLLALIEKGALGQKTGAGVYTKRGKDI 300

Query: 300 KVLDAKTGQY-VDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358
            VLD +   Y   AG+   E+   + ++D A++   LR S++PQA+FLWA FRD FHY A
Sbjct: 301 LVLDLQAQDYRAQAGELDAEVAALLKERDPAKKFAALRASSHPQAKFLWACFRDTFHYSA 360

Query: 359 VYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPA 418
            +LE IA +A D+D A+RWG+GW+ GPFE WQ+AGWKQVAEW+ ED+  G A+S APLP 
Sbjct: 361 FHLESIADTARDVDFAMRWGYGWSMGPFESWQAAGWKQVAEWIAEDIVQGNAMSNAPLPN 420

Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTV 478
           WVF+G     +GVH  AGS+SP   + VARS  PVYQRQ F   + G    +    G TV
Sbjct: 421 WVFDG----REGVHGTAGSYSPGRNTMVARSANPVYQRQRFPDPLLG----EKFSQGVTV 472

Query: 479 EENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538
            END VR+W  +G DD+ VVSFK+KM+T+   V+DGL +A+ +AE  +KGLV+WQP    
Sbjct: 473 YENDGVRMWADDG-DDIAVVSFKTKMHTVSDAVLDGLQQAVAIAEQKFKGLVIWQPKE-- 529

Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598
                 PFSAGA+L  A+ A   G     E  V  FQ    R+KYA VPVV+A  G+ALG
Sbjct: 530 ------PFSAGADLAGALGALQAGKIAEFEAMVANFQATSQRIKYAQVPVVAAVRGMALG 583

Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLT 658
           GGCE  +HSA  V ALE+YIGLVE GVGL+PAGGGLKE A+ A+  A   G  ++   L 
Sbjct: 584 GGCEFQMHSARTVLALESYIGLVEAGVGLLPAGGGLKEFAVRASEKAGPNG--DVFAELK 641

Query: 659 SRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT- 717
           + F+S AM KVSASA EAR +   + SD +VFN HELLYVA+ + RALA +GYR PLP  
Sbjct: 642 TAFESVAMGKVSASAFEARNLKLARDSDVVVFNAHELLYVAKQQARALAESGYRPPLPAR 701

Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777
            + VAG  GIAT K  LVNM +G FIS HD+ IA+RIA  VCGG+V+ G++V E+WLL L
Sbjct: 702 AIRVAGDVGIATFKMLLVNMLEGRFISPHDYEIATRIATVVCGGEVDRGAVVDEEWLLKL 761

Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           ER+ FV L    KTQERI  ML+TGKP+RN
Sbjct: 762 EREHFVALAQMPKTQERIAHMLKTGKPLRN 791


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: 1554
Number of extensions: 51
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: 791
Length adjustment: 41
Effective length of query: 766
Effective length of database: 750
Effective search space:   574500
Effective search space used:   574500
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