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 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 (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