Alignments for a candidate for ech in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Dechlorosoma suillum PS

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 Dsui_0323 Dsui_0323 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__PS:Dsui_0323
          Length = 645

 Score =  175 bits (443), Expect = 7e-48
 Identities = 121/343 (35%), Positives = 181/343 (52%), Gaps = 15/343 (4%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSK-LRESGSLKEGV 60
           +V V+G+GVMG  IA   A  G  V + D + E +  A++R     ++ +R+   L+   
Sbjct: 308 RVHVVGAGVMGGDIAAWCAGRGLTVTLQDQNVERIAPAIKRAHAGFARRIRDKLQLRA-- 365

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
             V+ R+ P+ +   A   +D VIEA+ E+LE K ++ +  EA   P AVLATNTSSL +
Sbjct: 366 --VMDRLIPDPEGHGAAH-ADVVIEAIFENLEAKHSLLKGLEARMKPDAVLATNTSSLKL 422

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
            +I +VL+ P+R+VG+HFFNP   MPLVE+V       EV +      + ++K  + V+ 
Sbjct: 423 EDIRTVLQRPERLVGIHFFNPVAKMPLVEVVTAAGGDAEVTRQACAFVRGIDKLPLPVQS 482

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
            PGF VN VL   +      V++GIA  + VD +A+   G PMG   LAD  GLDI  + 
Sbjct: 483 APGFLVNAVLGPYLLEAMRCVDEGIAP-ETVDEAAL-AFGMPMGPIELADTVGLDIAMAA 540

Query: 241 WKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLPSTSKKLGRYLI 300
            KA+   G +  P     +   +G LG KSG G+Y YP+ GK  +    +    L   L+
Sbjct: 541 GKALAGNGTE--PPKCLVQRFERGDLGRKSGKGFYAYPA-GKIQKGAAGAVPAGLAERLV 597

Query: 301 SPAVNEVSYLLREGIVGKDD-AEKGCVLGLGLPK---GILSYA 339
            P +     L+  G+V   + A+ G + G G      G L+YA
Sbjct: 598 QPLLQRTQQLVDAGVVADAELADAGVIFGTGFAPFTGGPLNYA 640



 Score =  100 bits (248), Expect = 3e-25
 Identities = 67/197 (34%), Positives = 109/197 (55%), Gaps = 9/197 (4%)

Query: 407 LAWIVLNRPTRY-NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGS 465
           LAW+ L++     N+++  ++ E++  LD L+ +    +I  + +   F AGAD++EF  
Sbjct: 23  LAWLSLDKAGESANSLSKAVMAELSGVLDELDRQPPKALIIRSAKSAGFIAGADISEFDQ 82

Query: 466 LTP---VKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSAD--FRVASKTA 520
           L      KAM+A  +  E+F ++  +  P +A++ G  LGGG+ELAL+      V     
Sbjct: 83  LDSPEAAKAMVA--RGWELFNRLAAVPYPTLALVRGHCLGGGLELALACRTLLVVDEPGT 140

Query: 521 EMGQPEINLGLIPGGGGTQRLSRLSGRK-GLELVLTGRRVKAEEAYRLGIVEFLAEPEEL 579
           ++G PE+ LG+ PG GG  RL R  G    L+L+L G+ V A++A RLG+ +    P  +
Sbjct: 141 KLGLPEVMLGIFPGWGGMLRLPRRVGPAVALDLMLAGKTVDAKKAKRLGLADECVPPRVM 200

Query: 580 ESEVRKLANAIAEKSPL 596
           ES  R+LA     + PL
Sbjct: 201 ESAARQLALNPPSRKPL 217



 Score = 42.7 bits (99), Expect = 5e-08
 Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 6/91 (6%)

Query: 299 LISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTS 358
           ++ P + E    + EGI  +   E    L  G+P G +  AD +G+D+ +   + +    
Sbjct: 491 VLGPYLLEAMRCVDEGIAPETVDE--AALAFGMPMGPIELADTVGLDIAMAAGKALAGNG 548

Query: 359 GMDHYSPDPLLLSMVKEGKLGRKSGQGFHTY 389
                 P   L+   + G LGRKSG+GF+ Y
Sbjct: 549 T----EPPKCLVQRFERGDLGRKSGKGFYAY 575


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: 844
Number of extensions: 36
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: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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