GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-beta in Sphingomonas koreensis DSMZ 15582

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Ga0059261_1453 Ga0059261_1453 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs

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



>FitnessBrowser__Korea:Ga0059261_1453
          Length = 740

 Score =  280 bits (715), Expect = 2e-79
 Identities = 221/725 (30%), Positives = 340/725 (46%), Gaps = 70/725 (9%)

Query: 48  ERGTQVPAFLEIRPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEA 107
           ++ T   A+L+I  +G V +  P  E GQG  T + Q++ ++L AD     VE AP    
Sbjct: 42  DKETAFGAWLKIAENGQVTVAIPQCEYGQGVFTTLPQLLADQLGADWRMVGVEQAPLNPI 101

Query: 108 YV---------------------VMENGLRITGGSMSVRMSYPTMRRLGALARAMLLQAG 146
           Y                         N   +TGGS S+R     +R  GA ARA+L +A 
Sbjct: 102 YANSLALDALFPGVFPERLKRIWAERNLAMLTGGSTSMRSFETPLRSAGAGARALLCKAA 161

Query: 147 AKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPDPASITLRDPSQFRWIGK 206
           A++WGV   E  T  G VVH    + L +GELA+ A    +PD   +  R+    R  G 
Sbjct: 162 ARRWGVDWQECDTANGHVVH--DQKRLRFGELAAEAAGEKLPD--DLPFREGETGRLTGT 217

Query: 207 PVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRNQSQVEGMKGVHSVH 266
           P  RLD   K  G A ++ D+++  M+ AA++  P +G    +  +++    + G+  +H
Sbjct: 218 PAPRLDGPGKVDGSANFAADIRLPGMVFAALRQGP-IGTVKLAAIDEAAAAKVPGM--LH 274

Query: 267 VLPGA--VAVVAERWWHAKRAVEAIQVDWQEAA---ADSALRVMPADFSSDKHREFLAAQ 321
           ++     VA VA  WW A +A++AI   ++ AA   +++    + A   SD  R   A  
Sbjct: 275 IVKNELWVATVANNWWAASQALDAISPRFEVAAKVESETIQAALDAALESDGERMASA-- 332

Query: 322 QGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQ 381
                     GD+A   K A+  V A Y      HA +EP  A A +  +G + +WLP Q
Sbjct: 333 ----------GDLAPVFKDARV-VAAEYRVGLALHAAIEPICATAVWE-EGRVRLWLPTQ 380

Query: 382 APDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAKAVSRPIKLI 441
           AP   R  +A   G+  + + +H  L GG FG++  + +A    QA  +A+ V +P++L+
Sbjct: 381 APGFARDAVANVLGVSASDVVIHPMLAGGSFGQNLEHQAA---AQAALIAREVKKPVQLM 437

Query: 442 WSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEALA-------GKQGDK 494
           WSR E  ++D  RP AV +  A L   G      A  A       LA       G  G  
Sbjct: 438 WSRGETCVQDRFRPPAVGRMTARLGANGSISGWLAKIAAPRTGHELARRLTGGGGATGAA 497

Query: 495 IDPTAVEGLSGKSYAIPNKRIAQIYVKGAPM-----LGYWRSVGNSLNDFFYESFLDELA 549
           +    +   +  + A P  RI  + +   P+      GYWRS  +S   FF ESF+DELA
Sbjct: 498 LATGGIGDAAAVAGARPPYRIPALAIDHHPVEIVVPTGYWRSGAHSYTAFFTESFIDELA 557

Query: 550 DKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGS 609
                + +  R+ +L   PRL   L     L GGW+ G           +G+A  +  GS
Sbjct: 558 HVADIEAFSFRIAMLGGEPRLARCLSTVTSL-GGWQGGL------PGSGQGLACHAFGGS 610

Query: 610 HTAAIAEVSIENG-KVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVD 668
           + A +AE S+    +V+V  +  A+D G +VNP++VE Q+ G +  G++  L        
Sbjct: 611 YIAVMAEASVGGDQRVQVDRLIAAVDCGRVVNPSVVEQQIEGGLIFGMAAALGATTGITA 670

Query: 669 GKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRV 728
            +P AR++    +   A   ++ V ++ S    GG  E  +P VAPA+ANA+   TG R+
Sbjct: 671 NRPEARSFRDLELPRLADCPQIMVELIASDADPGGASELAVPPVAPAIANALYAATGVRL 730

Query: 729 RSLPL 733
           R LPL
Sbjct: 731 RQLPL 735


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: 1308
Number of extensions: 78
Number of successful extensions: 7
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: 740
Length adjustment: 40
Effective length of query: 699
Effective length of database: 700
Effective search space:   489300
Effective search space used:   489300
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:

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