GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuD in Caulobacter crescentus NA1000

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate CCNA_02054 CCNA_02054 methylmalonyl-CoA carboxylase, carboxyltransferase subunit

Query= BRENDA::Q9LDD8
         (587 letters)



>lcl|FitnessBrowser__Caulo:CCNA_02054 CCNA_02054 methylmalonyl-CoA
           carboxylase, carboxyltransferase subunit
          Length = 510

 Score =  273 bits (698), Expect = 1e-77
 Identities = 165/506 (32%), Positives = 265/506 (52%), Gaps = 32/506 (6%)

Query: 68  MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE- 126
           M+ IL EL    ++  AGGGE  V    ++ KL  RERI+ LLD GS F E      H  
Sbjct: 1   MQHILEELERRRQQAKAGGGETRVASQHAKGKLTARERIELLLDEGS-FEEFDMFVEHRC 59

Query: 127 ----LYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182
               + ++ +P  G++TG G I+G++    + D TV GG+      +K ++ Q  A +  
Sbjct: 60  ADFGMQDQKIPGDGVVTGWGTINGKVVYVFSKDFTVFGGSLSNAHAQKIVKVQRQAMKVG 119

Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242
            P I L D+GGA + +  +       +  +F  E+VM+S  IPQI++++G C  G  Y P
Sbjct: 120 APVIGLFDAGGARIQEGVDSLA---GYADIFV-ENVMASGVIPQISVIMGPCAGGDVYSP 175

Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302
           AM D   MVK    +F+ GP +VK  T E V+AE+LGGA VH   SGV++   +++L  +
Sbjct: 176 AMTDFIFMVKDTSYMFVTGPDVVKTVTNEVVTAEELGGARVHAAKSGVAEGAFENDLEAM 235

Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSIIARI 362
              R ++  L  + ++        +   + EPL D   L ++ P D  + +D++ +I ++
Sbjct: 236 TQVRRLIDFLPSSNREP-----APERESFDEPLRDEMSLDTLVPADPTKPYDMKELILKV 290

Query: 363 VDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCSQ 417
           VD ++F E   ++   ++ GFAR+ G+TVGI+ N      G+L  +S+ K A F+  C  
Sbjct: 291 VDEADFFEISSEWAKNIICGFARMDGETVGIVANQPQVLAGVLDIDSSRKAARFVRFCDA 350

Query: 418 RKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAMC 477
             IP+V   ++ GFM G++ E  G+ K GAK++ A + A VPKIT+IT  ++G     M 
Sbjct: 351 FNIPIVTFVDVPGFMPGTKQEYGGLIKHGAKLLFAYTEATVPKITVITRKAYGGAYDVMS 410

Query: 478 GRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDAY 537
            +    D  + WP A I +MG   A  ++ + E             ++ EA   +  +  
Sbjct: 411 SKHLRGDLNYAWPTAEIAVMGAKGAVEIIFRQE------------AKDPEALAAREAEYK 458

Query: 538 EREANPYYSTARLWDDGVIDPCDTRK 563
           +R ANP+ +  R + D VI P  TR+
Sbjct: 459 DRFANPFVAAQRGYIDDVIMPHGTRR 484


Lambda     K      H
   0.320    0.138    0.408 

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: 728
Number of extensions: 36
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: 587
Length of database: 510
Length adjustment: 36
Effective length of query: 551
Effective length of database: 474
Effective search space:   261174
Effective search space used:   261174
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 preprint 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