GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Dechlorosoma suillum PS

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Dsui_0517 Dsui_0517 acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)

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



>FitnessBrowser__PS:Dsui_0517
          Length = 510

 Score =  262 bits (669), Expect = 3e-74
 Identities = 176/501 (35%), Positives = 260/501 (51%), Gaps = 30/501 (5%)

Query: 22  MAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARVEKLLDPGSPFLELSQFAA--- 78
           M  ++ +L+ K      GGG   ++    +GKL  R R+E LLDP S F E   F     
Sbjct: 1   MHDIIHELEKKREAARLGGGQKRIDSQHKKGKLTARERLELLLDPDS-FEEWDMFKEHRC 59

Query: 79  --FEVYDEDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPITVKKHLRAQAIAERCH 136
             F + +   P  G++ G G ++G    + + D TV GG+      +K  +    A +  
Sbjct: 60  TDFGMAETKNPGDGVVTGYGTINGRLVFVFSQDFTVFGGSLSETHAEKICKVMDHAMKVG 119

Query: 137 LPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKG-IPQIAVVMGLCTAGGAYV 195
            P I L DSGGA +    E       +  +F  Q  + A G IPQI+++MG C  G  Y 
Sbjct: 120 APVIGLNDSGGARI---QEGVASLGGYADVF--QRNVMASGVIPQISMIMGPCAGGAVYS 174

Query: 196 PAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTKISGVADHLAQNDEHA 255
           PAM D   +V++   +F+ GP +VK  T EEV+AEELGG   HT  SGVAD   +ND  A
Sbjct: 175 PAMTDFIFMVKDSSYMFVTGPEVVKTVTHEEVTAEELGGAVTHTTKSGVADLAFENDVEA 234

Query: 256 LELARKAVSRLNHQKQVELQLSKVKPPKYDIN-ELYGIVGTDLKKPFDVKEVIARIVDDS 314
           L   R+ V+ L    + +  + K   P   ++  L  +V  +  KP+D+KE+I ++VDD 
Sbjct: 235 LNYLRRLVNFLPANNREKPPVQKTNDPAERLDFSLDTLVPDNANKPYDMKELIIKMVDDC 294

Query: 315 DFDEFKANYGTTLVCGFARIHGYPVGIVANN-----GILFSESAQKGAHFIELCCQRKIP 369
           DF E + +Y   ++ GFAR+ G+PVGIVAN      G L  +S+ K A F+  C    IP
Sbjct: 295 DFFEIQPDYAKNIITGFARMDGHPVGIVANQPLVLAGCLDIKSSIKAARFVRFCDAFNIP 354

Query: 370 LVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAGNYGMCGRAF 429
           +V L ++ GFM G   E+ GI KHGAK++ A +  TVPK T++   +YG     M  +  
Sbjct: 355 VVTLVDVPGFMPGTSQEYGGIIKHGAKLLYAYAECTVPKVTLITRKAYGGAYDVMSSKHL 414

Query: 430 EPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKFKAPIIAQYDKEG 489
              +   WP+A I+VMG + A  ++    K+  A+      AE EA++KA       K  
Sbjct: 415 RGDVNLAWPSAEIAVMGPKGAVEIIFREEKNDPAK-----LAEREAEYKA-------KFA 462

Query: 490 HPYHASARLWDDGIIDPAQTR 510
           +P+ A AR + D +I P +TR
Sbjct: 463 NPFVAGARGFIDDVIMPNETR 483


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: 707
Number of extensions: 35
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: 535
Length of database: 510
Length adjustment: 35
Effective length of query: 500
Effective length of database: 475
Effective search space:   237500
Effective search space used:   237500
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.

Links

Downloads

Related tools

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