GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS21100
          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:

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