GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Cupriavidus basilensis 4G11

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate RR42_RS14490 RR42_RS14490 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Cup4G11:RR42_RS14490
          Length = 901

 Score =  667 bits (1721), Expect = 0.0
 Identities = 363/861 (42%), Positives = 521/861 (60%), Gaps = 44/861 (5%)

Query: 34  AYAKLPYTSRVLAENLVRRCEPEMLT-------ASLKQIIESKQELDFPWFPARVVCHDI 86
           A  +LP + RV+ E+++R C+ + +T       A  K + E   E+  P+  ARVV  D 
Sbjct: 35  AVERLPVSIRVVLESVLRNCDGKKVTEEHVRQLAHWKPVAERVDEI--PFVVARVVLQDF 92

Query: 87  LGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIED 146
            G   L DLA +R+     G +P ++ P+VP  L+VDHS+ +++   +K+A   N  +E 
Sbjct: 93  TGVPLLADLAAMRNVAEKMGKNPKKIEPLVPVDLVVDHSVQIDHFR-EKNALDLNMKLEF 151

Query: 147 RRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSH 206
           +RN +R+ F+ W  +AF    V+  G GI+HQ+NLE ++  +H ++GV +PDTLVGTDSH
Sbjct: 152 QRNNERYQFMKWGMQAFDTFGVVQPGFGIVHQVNLEYLARGVHKKDGVYYPDTLVGTDSH 211

Query: 207 TPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEF 266
           T  ++ +GV+  GVGG+EAE+ MLG+  Y   PD++GVEL G+ + G+TATD+VL +TE 
Sbjct: 212 TTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVELKGRLREGVTATDLVLTITEM 271

Query: 267 LRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREA 326
           LR +KVV  ++EFFGEG  +L L DRATI NM PE+GAT   F +D++T+DY   TGR  
Sbjct: 272 LRREKVVGKFVEFFGEGTASLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTE 331

Query: 327 EQVKLVETYAKTAGLWS-DDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARV--------- 376
           E++   E Y +   ++      +  Y   +  DL +V  ++AGP  P  R+         
Sbjct: 332 EEIAAFEGYFRAQKMFGVPKAGEIDYTNVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTF 391

Query: 377 ------PTSELAARGISGEVEN-----EPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLL 425
                 PT+E        E++      +   +  G V+IAAITSCTNTSNP  ++AAGLL
Sbjct: 392 ASLFAKPTAENGFNKDIAELDKTYTTADGVNVKSGDVLIAAITSCTNTSNPSVLLAAGLL 451

Query: 426 ARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGA 485
           A+ A   GL   P +KTSLAPGS+ V  YL+ A LLP LE LGFG+  + CTTC G +G 
Sbjct: 452 AKKAVEAGLKVAPHIKTSLAPGSRVVTEYLQAAGLLPYLEKLGFGVTAYGCTTCIGNAGD 511

Query: 486 LDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEK 545
           L P + + +   DL A AVLSGNRNF+ RIHP  +  FLASPPLVVAYAIAG +  D+  
Sbjct: 512 LTPELNEAITRNDLVAAAVLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNVTRDLMT 571

Query: 546 DVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPM---FDLSVDYGDKVSP 602
           + +G  K G+ + L +IWP+  EI A++  ++  + F+  YE +     L          
Sbjct: 572 EPVGTGKGGREIYLGDIWPTSEEIHALMKYAMDSKVFKINYEQVKKPSKLWAKVKGTKGQ 631

Query: 603 LYDWRPQSTYIRRPPYWEG----ALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSA 658
           +YDW P+STYI  PP+++G      A + +++  R L V GD++TTDH+SP+ +I   S 
Sbjct: 632 VYDW-PKSTYIAEPPFFDGFGMEPAATQSSVRNARALGVFGDSVTTDHISPAGSIKESSP 690

Query: 659 AGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIV--DGKVKQGSLARIE 716
           AG+YL   G+ + DFNSY + RG+H    R TFAN ++KN M  V  DG   +G +   +
Sbjct: 691 AGKYLLANGVLKADFNSYGSRRGNHEVMMRGTFANVRIKNLMLPVKADGSRVEGGVTLHQ 750

Query: 717 PEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIH 776
           P G    +++A   Y+    P ++  G +YG GSSRDWAAKG +L GV+A++   FERIH
Sbjct: 751 PSGEALSIYDAAMKYIAEGTPTVVFGGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIH 810

Query: 777 RTNLVGMGVLPLEFKAGENRATYGIDGTEVFD---VIGSIAPRADLTVIITRKNGERVEV 833
           R+NLVGMGVLPL+FK  ++  T GI G E FD   + G + P+ D+T++I R NG+   V
Sbjct: 811 RSNLVGMGVLPLQFKGSDSVQTLGIVGDETFDIEGIEGELKPQQDVTLVIKRANGDVQRV 870

Query: 834 PVTCRLDTAEEVSIYEAGGVL 854
           P+  R+DT  EV  Y  GG+L
Sbjct: 871 PLLLRIDTPIEVDYYNHGGIL 891


Lambda     K      H
   0.318    0.136    0.397 

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: 2000
Number of extensions: 103
Number of successful extensions: 10
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: 867
Length of database: 901
Length adjustment: 43
Effective length of query: 824
Effective length of database: 858
Effective search space:   706992
Effective search space used:   706992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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