Aligments for a candidate for pimF in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Aligments 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:

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 paper from 2022 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

GapMind for catabolism of small carbon sources