GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuD in Azospirillum brasilense Sp245

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate AZOBR_RS21100 AZOBR_RS21100 methylmalonyl-CoA carboxyltransferase

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



>lcl|FitnessBrowser__azobra:AZOBR_RS21100 AZOBR_RS21100
           methylmalonyl-CoA carboxyltransferase
          Length = 510

 Score =  243 bits (621), Expect = 1e-68
 Identities = 175/520 (33%), Positives = 261/520 (50%), Gaps = 36/520 (6%)

Query: 22  MAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARVEKLLDPGSPFLELSQFAAFEV 81
           M  ++A L    +    GGG   +    ++GKL  R R+E  LD GS F E   F     
Sbjct: 1   MQEILAKLDAMRSGARLGGGEKRVAGQHAKGKLTARERIELFLDEGS-FEEFDMFVQHRC 59

Query: 82  YD-----EDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPITVKKHLRAQAIAERCH 136
            D     + VP  G++ G G V+G    + + D TV GG+      +K  +    A +  
Sbjct: 60  NDFGMEGQKVPGDGVVTGHGTVNGRLVFVFSQDFTVFGGSLSEAHAEKICKIMDQAMKVG 119

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

Query: 196 PAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTKISGVADHLAQNDEHA 255
           PAM D   +V++   +F+ GP +VK  T E V+AEELGG   H+  SGVAD   +ND  A
Sbjct: 175 PAMTDFIFMVKDSSYMFVTGPDVVKTVTHEVVTAEELGGAITHSSKSGVADMAFENDVEA 234

Query: 256 LELARKAVSRL---NHQKQVELQLSKVKPPKYDINELYGIVGTDLKKPFDVKEVIARIVD 312
           L   R+ +  L   N ++  E   +   P   D   L  +V  +  KP+D+KE+I + VD
Sbjct: 235 LLQLRRFIDFLPASNRERAPERPTAD--PIDRDDLSLDTLVPENPNKPYDMKELILKTVD 292

Query: 313 DSDFDEFKANYGTTLVCGFARIHGYPVGIVANN-----GILFSESAQKGAHFIELCCQRK 367
           + DF E + +Y   ++ GF R++G  VGIVAN      G L  +S++K A F+  C   +
Sbjct: 293 EGDFFELQPDYAKNIIIGFGRMNGGTVGIVANQPMVLAGCLDIDSSKKAARFVRFCDAFE 352

Query: 368 IPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAGNYGMCGR 427
           IP++ L ++ GFM G   E+ GI KHGAK++ A + ATVPK TV+   +YG     M  +
Sbjct: 353 IPILTLVDVPGFMPGTSQEYGGIIKHGAKLLFAYAEATVPKITVITRKAYGGAYDVMASK 412

Query: 428 AFEPTLMWMWPNARISVMGGEQAAGVLATVRKD-GLARKGETMSAEEEAKFKAPIIAQYD 486
                + + WP+A I+VMG + A  ++   R D G   K E  + E   KF         
Sbjct: 413 HLRGDINYAWPSAEIAVMGPKGAVEII--FRGDIGDTAKIEARTEEYRQKF--------- 461

Query: 487 KEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIE 526
              +P+ A++R + D +I P  TR  +  A+S   N  ++
Sbjct: 462 --ANPFVAASRGYIDDVIMPHGTRRRVIKALSMLKNKQLQ 499


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: 676
Number of extensions: 38
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: 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 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