GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__PS:Dsui_0323 Dsui_0323 3-hydroxyacyl-CoA
           dehydrogenase
          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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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