GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Shewanella oneidensis MR-1

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 201058 SO1896 3-methylcrotonyl CoA carboxylase, beta subunit (NCBI ptt file)

Query= reanno::SB2B:6937191
         (535 letters)



>FitnessBrowser__MR1:201058
          Length = 535

 Score =  990 bits (2559), Expect = 0.0
 Identities = 489/535 (91%), Positives = 512/535 (95%)

Query: 1   MTQLTSRVNPRSDEFKQKHDAMAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARV 60
           MTQL+SR+N RSDEFK K D MAALVADLK KLA IE GGG VA+ERHLSRGK  PR RV
Sbjct: 1   MTQLSSRINARSDEFKAKSDDMAALVADLKTKLAKIELGGGPVALERHLSRGKRLPRQRV 60

Query: 61  EKLLDPGSPFLELSQFAAFEVYDEDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI 120
           EKLLD GSPFLELSQFAAFEVYDE+VPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI
Sbjct: 61  EKLLDAGSPFLELSQFAAFEVYDEEVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI 120

Query: 121 TVKKHLRAQAIAERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQ 180
           TVKKH+RAQ IA RCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIF+NQA+MSAKGIPQ
Sbjct: 121 TVKKHIRAQEIASRCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFYNQAQMSAKGIPQ 180

Query: 181 IAVVMGLCTAGGAYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTK 240
           IAVVMGLCTAGGAYVPAMADESIIV++QGTIFLAGPPLVKAATGEEVSAEELGG DVHTK
Sbjct: 181 IAVVMGLCTAGGAYVPAMADESIIVKDQGTIFLAGPPLVKAATGEEVSAEELGGADVHTK 240

Query: 241 ISGVADHLAQNDEHALELARKAVSRLNHQKQVELQLSKVKPPKYDINELYGIVGTDLKKP 300
           ISGVADHLAQNDEHALELAR+AVSRLNHQK++ L+LS VKPPK+DI+ELYGIVGTDLKKP
Sbjct: 241 ISGVADHLAQNDEHALELARRAVSRLNHQKEITLRLSPVKPPKFDISELYGIVGTDLKKP 300

Query: 301 FDVKEVIARIVDDSDFDEFKANYGTTLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI 360
           FDVKEVIARIVDDSDFDEFKANYG TLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI
Sbjct: 301 FDVKEVIARIVDDSDFDEFKANYGATLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI 360

Query: 361 ELCCQRKIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAG 420
           ELCCQRKIPL+FLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCA VPKFTV+IGGSYGAG
Sbjct: 361 ELCCQRKIPLLFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCANVPKFTVIIGGSYGAG 420

Query: 421 NYGMCGRAFEPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKFKAP 480
           NYGMCGRAFEPT+MWMWPNARISVMGGEQAAGVLATVR+DGLARKGE  SAE+E  FKAP
Sbjct: 421 NYGMCGRAFEPTMMWMWPNARISVMGGEQAAGVLATVRRDGLARKGEEWSAEDEKAFKAP 480

Query: 481 IIAQYDKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFGVFRM 535
           IIAQYDKEGHPYHASARLWDDGIIDPAQTRDV+GLA+SAALNAPIE+TRFGVFRM
Sbjct: 481 IIAQYDKEGHPYHASARLWDDGIIDPAQTRDVVGLALSAALNAPIEDTRFGVFRM 535


Lambda     K      H
   0.320    0.137    0.405 

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: 1125
Number of extensions: 44
Number of successful extensions: 1
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: 535
Length of database: 535
Length adjustment: 35
Effective length of query: 500
Effective length of database: 500
Effective search space:   250000
Effective search space used:   250000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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