GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Methylocystis bryophila S285

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_085772004.1 B1812_RS13170 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_002117405.1:WP_085772004.1
          Length = 728

 Score =  176 bits (446), Expect = 3e-48
 Identities = 125/404 (30%), Positives = 201/404 (49%), Gaps = 38/404 (9%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGV- 60
           K+ V+G+G MG G+  ++A+ G EV + D      Q++ ++ K ++ KL  SG +  G  
Sbjct: 329 KIGVLGAGFMGAGVGYVSALNGLEVVLIDRD----QESADKGKATIDKLI-SGQVSRGKA 383

Query: 61  -----EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNT 115
                E +LAR+    D  + LKG D ++EAV ED  +K    + A+A   P  V A+NT
Sbjct: 384 TASAKEALLARVEATPDY-ERLKGCDLILEAVFEDRAVKAEATKRAQAAVGPDVVFASNT 442

Query: 116 SSLPISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKET 175
           S+LPI+ +A     P+  +G+HFF+P   M LVEI+ G+ TSD+ + T  +  + + K  
Sbjct: 443 STLPITSLAETSLKPENFIGVHFFSPVEKMLLVEIILGEKTSDKALATALDFVRMIKKTP 502

Query: 176 IVVKDVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLD 235
           IVV D  GFF NR +L  +  G  ++ +G+     +  +A    G P+G   L D  GLD
Sbjct: 503 IVVNDSRGFFANRCVLAYVREGQTMLVEGVP--PAMIENAARMAGMPVGPLSLNDEVGLD 560

Query: 236 IGYSVWKAVTARGFKAFPCSSTEKLV------SQGKLGVKSGSGYYQYPSPG-KFVRPTL 288
           +G+ + +A T +   A      ++ V        G+ G K+G G+Y YP+ G K + P L
Sbjct: 561 LGWKILQA-TKKDLGAAAVDPAQERVLGFLVEKNGRFGRKNGKGFYDYPASGKKTLWPGL 619

Query: 289 PSTSKKL------------GRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK--- 333
              ++K              R+L++ AV          +    +A+ G +LG G      
Sbjct: 620 AGLAEKTLDPDAIDVKELERRFLVAQAVEAARTFAEHVVTDPREADVGSILGFGFAPFTG 679

Query: 334 GILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           G LSY D +G+   V   + +    G   ++P  LL  M +EG+
Sbjct: 680 GALSYIDGMGLKAFVALCDTLAAKYG-PRFAPPQLLRDMAREGE 722



 Score = 73.6 bits (179), Expect = 3e-17
 Identities = 49/184 (26%), Positives = 88/184 (47%), Gaps = 18/184 (9%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVT--------------EFG 464
           N I  +++ E+ Q ++ +     ++   I      FS GAD++              E G
Sbjct: 28  NVITEEVMSELAQVVEKVAADAAIKGCVIASGKNAFSGGADLSMLQKSRAAHGKALGEKG 87

Query: 465 SLTPVKAMIAS-RKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKT--AE 521
           +    +    S RK  +++ +++   KP    I+G+ LGG  ELAL+   RV +     +
Sbjct: 88  AEEANRLFFESARKLSQLYRRLETCGKPFAIAIHGVCLGGAFELALACHHRVLADDDKTK 147

Query: 522 MGQPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEELE 580
           +G PE+ +GL PG GGTQR++R+      L+ +  G ++  + A   G+ + LA   E+ 
Sbjct: 148 VGLPEVKVGLFPGAGGTQRVARIMPTGDALQFLFKGEQLSGKAAKAAGLAQELAPQSEIV 207

Query: 581 SEVR 584
           S  +
Sbjct: 208 SRAK 211



 Score = 39.7 bits (91), Expect = 5e-07
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 330 GLPKGILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDP---LLLSMVKEGKLGRKSGQGF 386
           G+P G LS  DE+G+D+    L+  ++  G     P     L   + K G+ GRK+G+GF
Sbjct: 545 GMPVGPLSLNDEVGLDLGWKILQATKKDLGAAAVDPAQERVLGFLVEKNGRFGRKNGKGF 604

Query: 387 HTY 389
           + Y
Sbjct: 605 YDY 607


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: 975
Number of extensions: 48
Number of successful extensions: 8
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: 728
Length adjustment: 39
Effective length of query: 612
Effective length of database: 689
Effective search space:   421668
Effective search space used:   421668
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