GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Methylocapsa aurea KYG

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate WP_036260031.1 DL86_RS07960 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_000746085.1:WP_036260031.1
          Length = 736

 Score =  164 bits (414), Expect = 2e-44
 Identities = 129/401 (32%), Positives = 197/401 (49%), Gaps = 38/401 (9%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAM----ERIKWSLSKLRESGSLK 57
           +V ++G+G MG GIA + A AG E  + D       +      + I   + K R  G+ K
Sbjct: 329 RVGILGAGFMGAGIAYVTAGAGMEGVLIDRDQASADKGKAFCDQLISSQVLKGRAKGADK 388

Query: 58  EGVEQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSS 117
           E +   L RI    D    L G++ VIEAV ED  +K    R A A   P A+ A+NTS+
Sbjct: 389 EAL---LGRIKTSADYND-LAGAELVIEAVFEDRTVKAEATRKARAAIGPDAIFASNTST 444

Query: 118 LPISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIV 177
           LPI  +A    +P+  +G+HFF+P   M LVE++ G  T D  + T  +  +++ K  IV
Sbjct: 445 LPIGSLAEADSAPENFIGVHFFSPVEKMLLVEVILGAKTGDRALATALDYVRAIKKTPIV 504

Query: 178 VKDVPGFFVNRVLLRIMEAGCYLVEKGI--ASIQEVDSSAIEELGFPMGVFLLADYTGLD 235
           V D  GFF NR +   +  G  ++ +G   A I+ +   A    G P+G   L D  GLD
Sbjct: 505 VNDARGFFANRCVGNYIREGHLMLLEGAPPAMIENIAKMA----GMPVGPLALNDEVGLD 560

Query: 236 IGYSVWKAVTARGFKAFPCSSTEKL-----VSQGKLGVKSGSGYYQYPSPG-KFVRPTLP 289
           +   + +A       A    + E+L     V  G+LG K+G G+Y YPS G K + P L 
Sbjct: 561 LALKILEATKQDLGGAAIDLNQERLLKGLVVEHGRLGRKNGKGFYDYPSQGAKSLWPGLA 620

Query: 290 S------------TSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK--- 333
           +             ++   R+L+  A+ E +  + EG+V    +A+ G ++G G      
Sbjct: 621 ALQPTKCDPDAIDIAEFKHRFLVVQAL-EAARAIEEGVVTDPREADVGSIIGFGFAPFTG 679

Query: 334 GILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVK 374
           G+LSY D +G    V   + +RQT G + +SP  +L+ M K
Sbjct: 680 GVLSYIDGMGAANFVVLCDRLRQTYG-ERFSPPQILIDMAK 719



 Score = 85.1 bits (209), Expect = 1e-20
 Identities = 60/196 (30%), Positives = 95/196 (48%), Gaps = 20/196 (10%)

Query: 407 LAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466
           L W +  R    N I   +I E+ Q +D +     +    IT   + FS GAD++  G+ 
Sbjct: 18  LTWDMAGRSM--NVITPQVIDELEQVIDHVGAEAAITGCVITSGKQTFSGGADLSMLGAA 75

Query: 467 TPVKAMI--------ASRKFHE-------VFMKIQFLTKPVIAVINGLALGGGMELALSA 511
                          A+R F E       V+ K++   KP  A ING+ LGG  ELAL+ 
Sbjct: 76  AADYQTARQEKGEEEAARLFFESARRLSLVYRKLETCGKPFAAAINGVCLGGAFELALAC 135

Query: 512 DFRVAS--KTAEMGQPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLG 568
            +RV +    A +G PEI +GL PG GGTQR++RL      L+++  G +++ + A  + 
Sbjct: 136 HYRVVADDDKARVGLPEIKVGLFPGAGGTQRVARLMHTGDALQMLFKGEQIRPKAAKTMN 195

Query: 569 IVEFLAEPEELESEVR 584
           +V  +A   E+  + +
Sbjct: 196 LVHDVAPLGEIVGKAK 211



 Score = 47.4 bits (111), Expect = 2e-09
 Identities = 26/69 (37%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 330 GLPKGILSYADEIGIDVVVNTLEEMRQTSG---MDHYSPDPLLLSMVKEGKLGRKSGQGF 386
           G+P G L+  DE+G+D+ +  LE  +Q  G   +D      L   +V+ G+LGRK+G+GF
Sbjct: 545 GMPVGPLALNDEVGLDLALKILEATKQDLGGAAIDLNQERLLKGLVVEHGRLGRKNGKGF 604

Query: 387 HTYAHEEAK 395
           + Y  + AK
Sbjct: 605 YDYPSQGAK 613


Lambda     K      H
   0.316    0.134    0.377 

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: 979
Number of extensions: 47
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 736
Length adjustment: 39
Effective length of query: 612
Effective length of database: 697
Effective search space:   426564
Effective search space used:   426564
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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