GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_02054
          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:

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