Alignments for a candidate for ech in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Marivita geojedonensis DPG-138

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_085636206.1 MGEO_RS08035 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_002115805.1:WP_085636206.1
          Length = 728

 Score =  167 bits (424), Expect = 1e-45
 Identities = 120/400 (30%), Positives = 200/400 (50%), Gaps = 32/400 (8%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVE 61
           KV V+G+G+MG GIA ++A AG +V + D      Q A ++ K   +     G  +  + 
Sbjct: 324 KVGVLGAGMMGAGIALVSAQAGIDVVLLDRD----QAAADKGKAYSADYAAKGVSRRKIT 379

Query: 62  Q-----VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTS 116
           Q     +LARI   TD    L G D ++EAV ED ++K  +    EA      + ATNTS
Sbjct: 380 QDKADAMLARITATTDYND-LAGCDLIVEAVFEDPKIKADVTAQVEAVIGEDCIFATNTS 438

Query: 117 SLPISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETI 176
           +LPIS++A   K P++ +G+HFF+P   M LVEI++GK+T D  V    +  + + K  I
Sbjct: 439 TLPISDLAKASKRPEQFIGIHFFSPVEKMMLVEIIKGKETGDRAVAKALDFVRQIRKTPI 498

Query: 177 VVKDVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDI 236
           VV D   F+ NR ++  +  G  +V++G+A    +  +A + +G P+G   L D T +D+
Sbjct: 499 VVNDARFFYANRCIIPYINEGIRMVKEGVA--PALIENAAKMVGMPLGPLQLVDETSIDL 556

Query: 237 GYSVWKAVTARGFKAFPCSSTEKLV----SQGKLGVKSGSGYYQYPSPGK------FVRP 286
           G  + +A  A    A+P  + ++++     +G+LG K+ +G+Y Y   GK       V  
Sbjct: 557 GAKIARATKAAMGDAYPDGAVDEVIFWMEGEGRLGRKAKAGFYDYDDKGKRQGLSSVVAA 616

Query: 287 TLPSTSKK------LGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GILS 337
             P    +        R L   ++  V  L    ++   + + G +LG G      G LS
Sbjct: 617 QYPQAEDQPDLIDVQHRLLFVQSLEAVRALEDGVLMDIREGDVGAILGWGFAPWSGGPLS 676

Query: 338 YADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           + D +G +      +++ +T G D ++   LL  M  +G+
Sbjct: 677 WLDMLGSEYAAERCDQLVETYG-DRFACPDLLREMAAKGQ 715



 Score = 64.3 bits (155), Expect = 2e-14
 Identities = 53/174 (30%), Positives = 82/174 (47%), Gaps = 16/174 (9%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLTPVKAMIAS--- 475
           N ++ + ++ +N  +D     E V+ I IT     F+AG D+    +L    A       
Sbjct: 26  NVLSFEGLQTLNDLVDDALADEAVKGIIITSGKADFAAGMDLNVLATLKEAGAEAVFDGI 85

Query: 476 RKFHEVFMKIQFLT---------KPVIAVINGLALGGGMELALSAD--FRVASKTAEMGQ 524
            K H V  KI+            KPV AV+ G ALG G+E+ L+    F   +  A++G 
Sbjct: 86  MKMHGVLRKIERAGMDAKTNKGGKPVAAVLPGTALGIGLEIPLACHRVFAADNPKAKIGL 145

Query: 525 PEINLGLIPGGGGTQRLSRLSGRKGLE-LVLTGRRVKAEEAYRLGIV-EFLAEP 576
           PEI +G+ PG GGT R++R  G       +L G+     +A   G++ E  A+P
Sbjct: 146 PEILVGIFPGAGGTTRVARKMGAMAASPFLLEGKLSDPAKAKAAGLIDEVSADP 199



 Score = 39.7 bits (91), Expect = 5e-07
 Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 10/95 (10%)

Query: 300 ISPAVNEVSYLLREGIVGK--DDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQT 357
           I P +NE   +++EG+     ++A K     +G+P G L   DE  ID+        +  
Sbjct: 512 IIPYINEGIRMVKEGVAPALIENAAKM----VGMPLGPLQLVDETSIDLGAKIARATKAA 567

Query: 358 SGMDHY---SPDPLLLSMVKEGKLGRKSGQGFHTY 389
            G D Y   + D ++  M  EG+LGRK+  GF+ Y
Sbjct: 568 MG-DAYPDGAVDEVIFWMEGEGRLGRKAKAGFYDY 601


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: 969
Number of extensions: 50
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 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:

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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