GapMind for catabolism of small carbon sources

 

Aligments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2E3

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate AO353_23435 AO353_23435 twin-arginine translocation pathway signal protein

Query= metacyc::MONOMER-20833
         (739 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_23435 AO353_23435
           twin-arginine translocation pathway signal protein
          Length = 722

 Score =  422 bits (1084), Expect = e-122
 Identities = 289/745 (38%), Positives = 396/745 (53%), Gaps = 47/745 (6%)

Query: 8   LDAPVNLSRRRFLASTAV--GALVIGFGLPLGAGRVQAATSAERGTQVP-AFLEIRPDGT 64
           ++A +  SRR FL STAV    LV+ F +P GA R   A S       P AFL I PDG+
Sbjct: 1   MNAKIETSRRDFLKSTAVLGAGLVVAFVIP-GANRFAQAASTPDAVFAPNAFLRIAPDGS 59

Query: 65  VRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVME--NGLRITGGSM 122
           V +L    E GQG  T +  ++ EELDAD     VE AP   A   +    G++ITGGS 
Sbjct: 60  VTILLGHSEMGQGIWTGLTMLIAEELDADWTKIRVEHAPASAADYGLPAFGGMQITGGST 119

Query: 123 SVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSA 182
           S  M +   R+ GA AR ML++A AK++ V   ++ T+PG V+  A  +   YGELA+ A
Sbjct: 120 STWMEFDRYRQAGAAARLMLIEAAAKRFNVAPSKIQTEPGVVI--AGDQRATYGELANDA 177

Query: 183 LDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPR 242
             +PVPDPASI L+D   ++ IGKP KRLD  +K TG+A + +D++ D +L A V   P 
Sbjct: 178 GQLPVPDPASIKLKDAKDWKIIGKPTKRLDTPEKITGQAKFGMDVQFDGLLTAVVARPPV 237

Query: 243 LGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQ---EAAAD 299
            G +V S    + +  + GVH V  +P  +AVVA+ +W AK   +A+++DW     A  D
Sbjct: 238 FGGSVKSFDGAAAL-ALPGVHKVVQVPTGIAVVADHYWAAKLGRDALKIDWDLGPNAGLD 296

Query: 300 SALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQL 359
           S       D      R+  A    P       GD++ AL  A   ++  Y   YL HA +
Sbjct: 297 S-------DALLQNFRKLAAIPGTPA---SQAGDISAALSKAVKTIDVEYSVPYLAHAPM 346

Query: 360 EPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYD 419
           EP +   +  PD   EIW   Q   + +   AK TGL P Q+ +H+  LGG FGR     
Sbjct: 347 EPLNCTVKITPD-KCEIWTGTQFQTLDQMIAAKITGLKPEQVEIHTEFLGGGFGRR---- 401

Query: 420 SANP----YPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIE 475
            ANP      +A+ +AKA   P+K +WSRE++      R   +   R  LD KG+P A +
Sbjct: 402 -ANPTSDFVSEAVQVAKAAVAPVKTVWSREDDIRGGYYRSAFLHHARIGLDAKGMPQAWQ 460

Query: 476 AV----SATEG-PTEALAGKQGDKIDPTAVEGLSGKSY--AIPNKRIAQIYVKGAPMLGY 528
            V    S  +G P EA   K G  +D T+VEG++   Y   + N  +     K    + +
Sbjct: 461 HVLVGQSIMDGTPFEATMVKNG--VDATSVEGVADSPYIKGLANHLVDLHSPKTGISVLW 518

Query: 529 WRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGP 588
            RSVG++   F  ES +DELA   G DP E R  LL+++PR   +L  A E    WK  P
Sbjct: 519 MRSVGHTHTAFVVESLIDELATAAGKDPVEYRRTLLKEHPRHLGVLNLAVE-KANWK-AP 576

Query: 589 FTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQV 648
             A      A GVA+   FGS+ A +AEVS +N K++VH +  A+D G +VNPA + AQ+
Sbjct: 577 LPAG----HALGVAVHESFGSYVAQVAEVSQDNLKIRVHRVVCAVDCGVVVNPASIAAQM 632

Query: 649 NGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPP 708
              +  GL  TL  +  + DGK    NY  + +L   +M  V V +V S EK GGIGE  
Sbjct: 633 ESGITFGLGFTLHSKLTFKDGKVVQSNYHDFQVLRLNEMPVVEVHIVPSTEKPGGIGETG 692

Query: 709 LPAVAPAVANAVAQLTGQRVRSLPL 733
           +P  APAVANAV  LTGQR+R LPL
Sbjct: 693 VPPTAPAVANAVFALTGQRLRELPL 717


Lambda     K      H
   0.317    0.134    0.394 

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: 1286
Number of extensions: 52
Number of successful extensions: 10
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: 739
Length of database: 722
Length adjustment: 40
Effective length of query: 699
Effective length of database: 682
Effective search space:   476718
Effective search space used:   476718
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: 55 (25.8 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 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