GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Dechlorosoma suillum PS

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Dsui_0323 Dsui_0323 3-hydroxyacyl-CoA dehydrogenase

Query= metacyc::MONOMER-20678
         (699 letters)



>FitnessBrowser__PS:Dsui_0323
          Length = 645

 Score =  246 bits (627), Expect = 3e-69
 Identities = 198/642 (30%), Positives = 294/642 (45%), Gaps = 50/642 (7%)

Query: 24  NALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFGKPPQPPALNDVIAA 83
           N+LS AV   +   ++     P    I+       FIAGADI+EF +   P A   ++A 
Sbjct: 36  NSLSKAVMAELSGVLDELDRQPPKALIIRSAKSAGFIAGADISEFDQLDSPEAAKAMVAR 95

Query: 84  -------LENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKE--AKLGLPEVKLGLLPGA 134
                  L   P PT+A + G  LGGGLE+AL C   + V E   KLGLPEV LG+ PG 
Sbjct: 96  GWELFNRLAAVPYPTLALVRGHCLGGGLELALACRTLLVVDEPGTKLGLPEVMLGIFPGW 155

Query: 135 GGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVENLVAGAVAFAKKVLAEKRP 194
           GG  RLPR VGP +A+ +++ G  + A +A + GL +E V   V  + A   + LA   P
Sbjct: 156 GGMLRLPRRVGPAVALDLMLAGKTVDAKKAKRLGLADECVPPRVMESAA---RQLALNPP 212

Query: 195 LRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARG--LEAPFACADAIGAAIDLPFEEGLK 252
            R+      +L        +   A   + K+AR     AP+A  D + A  D     G  
Sbjct: 213 SRKPLPLLQRLFLGPLRGVVAGQARKQVAKRARPEHYPAPYAIID-LWAKYD-----GNA 266

Query: 253 KEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAM 312
                    +V   +       F  +E  K  G       +   RV ++GAG MGG IA 
Sbjct: 267 LAAPEITDRIVRSATARNLVRVFHLQERLKAFGKDSAFVAK---RVHVVGAGVMGGDIAA 323

Query: 313 SFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENV 372
             A  G+ VTL +   E++   +      + A   R  L   A   R  LI    G    
Sbjct: 324 WCAGRGLTVTLQDQNVERIAPAIKRAHAGF-ARRIRDKLQLRAVMDR--LIPDPEG-HGA 379

Query: 373 KDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMH 432
             AD++IEA+FE +  K  +   ++A  KP AVLA+NTS L +++I    +RP+ ++G+H
Sbjct: 380 AHADVVIEAIFENLEAKHSLLKGLEARMKPDAVLATNTSSLKLEDIRTVLQRPERLVGIH 439

Query: 433 FFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQS 492
           FF+P   M L E+V  A    +    A +  + I K+P+ V    GF+ N +L     ++
Sbjct: 440 FFNPVAKMPLVEVVTAAGGDAEVTRQACAFVRGIDKLPLPVQSAPGFLVNAVLGPYLLEA 499

Query: 493 EKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKD-RGIKSEIADALC--- 548
            + + EG  P+ VD     FGMPMGP  + D  GLDI   + K   G  +E    L    
Sbjct: 500 MRCVDEGIAPETVDEAALAFGMPMGPIELADTVGLDIAMAAGKALAGNGTEPPKCLVQRF 559

Query: 549 EAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPM 608
           E G  G+K+GKG+Y Y  G                   K+           + ER+V P+
Sbjct: 560 ERGDLGRKSGKGFYAYPAG-------------------KIQKGAAGAVPAGLAERLVQPL 600

Query: 609 INEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADS 650
           +    ++++  + A     D   ++G G+  + GGP++YA S
Sbjct: 601 LQRTQQLVDAGVVADAELADAGVIFGTGFAPFTGGPLNYARS 642


Lambda     K      H
   0.317    0.134    0.383 

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: 993
Number of extensions: 51
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 699
Length of database: 645
Length adjustment: 39
Effective length of query: 660
Effective length of database: 606
Effective search space:   399960
Effective search space used:   399960
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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:

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