GapMind for catabolism of small carbon sources

 

Aligments for a candidate for odc in Escherichia coli BW25113

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate 14332 b0186 lysine decarboxylase 2, constitutive (NCBI)

Query= BRENDA::P21169
         (711 letters)



>lcl|FitnessBrowser__Keio:14332 b0186 lysine decarboxylase 2,
           constitutive (NCBI)
          Length = 713

 Score =  322 bits (825), Expect = 4e-92
 Identities = 211/620 (34%), Positives = 311/620 (50%), Gaps = 44/620 (7%)

Query: 94  QYEENLLPPFYDTLTQYVEMGNSTFACPGHQHGAFFKKHPAGRHFYDFFGENVFRADMCN 153
           +Y +N+ PPF   L  YV+    TF  PGH  G  ++K P G  FYDFFG N  +AD+  
Sbjct: 123 EYLDNITPPFTKALFTYVKERKYTFCTPGHMGGTAYQKSPVGCLFYDFFGGNTLKADVSI 182

Query: 154 ADVKLGDLLIHEGSAKDAQKFAAKVFHADKTYFVLNGTSAANKVVTNALLTRGDLVLFDR 213
           +  +LG LL H G   +A+++ A+ F A+++Y V NGTS +NK+V       G  +L DR
Sbjct: 183 SVTELGSLLDHTGPHLEAEEYIARTFGAEQSYIVTNGTSTSNKIVGMYAAPSGSTLLIDR 242

Query: 214 NNHKSNHHGALIQAGATPVYLEASRNPFGFIGGIDAHCFNEEYLRQQIRDVAPEKADLPR 273
           N HKS  H  L+     PV+L+ +RN  G +GGI    F  + + +++   A  +A  P 
Sbjct: 243 NCHKSLAH-LLMMNDVVPVWLKPTRNALGILGGIPRREFTRDSIEEKV--AATTQAQWPV 299

Query: 274 PYRLAIIQLGTYDGTVYNARQVIDTVGHLCDYILFDSAWVGYEQFIPMMADSSPLLLELN 333
               A+I   TYDG +YN   +  T+      I FDSAWV Y  F P+    S +  E  
Sbjct: 300 H---AVITNSTYDGLLYNTDWIKQTLD--VPSIHFDSAWVPYTHFHPIYQGKSGMSGE-R 353

Query: 334 ENDPGIFVTQSVHKQQAGFSQTSQIHKKDNHIRGQARFCPHKRLNNAFMLHASTSPFYPL 393
                IF TQS HK  A  SQ S IH K  +          +  N AFM+H +TSP YP+
Sbjct: 354 VAGKVIFETQSTHKMLAALSQASLIHIKGEY--------DEEAFNEAFMMHTTTSPSYPI 405

Query: 394 FAALDVNAKIHEGESGRRLWAECVEIGIEARKAILARCK-----LFRPFIPPVVDGKLWQ 448
            A+++  A +  G  G+RL    VE  +  RK +    +      F  + PP VD     
Sbjct: 406 VASVETAAAMLRGNPGKRLINRSVERALHFRKEVQRLREESDGWFFDIWQPPQVD----- 460

Query: 449 DYPTSVLASDRRFFSFEPGAKWHGFEGYAADQYFVDPCKLLLTTPGIDAETGEYSDFGVP 508
                    +   +   PG +WHGF    AD  F+DP K+ + TPG+D E G  S+ G+P
Sbjct: 461 ---------EAECWPVAPGEQWHGFNDADADHMFLDPVKVTILTPGMD-EQGNMSEEGIP 510

Query: 509 ATILAHYLRENGIVPEKCDLNSILFLLTPAESHEKLAQLVAMLAQFEQHIEDDSPLVEVL 568
           A ++A +L E GIV EK    ++LFL +      K   L+  L +F++  + +  +  +L
Sbjct: 511 AALVAKFLDERGIVVEKTGPYNLLFLFSIGIDKTKAMGLLRGLTEFKRSYDLNLRIKNML 570

Query: 569 PSVYNKYPVRYRDYTLRQLCQEMHDLYVSFDVKDLQKAMFRQQSFPSVVMNPQDAHSAYI 628
           P +Y + P  YR+  ++ L Q +H L    D+  L    F   + P ++M P  A    I
Sbjct: 571 PDLYAEDPDFYRNMRIQDLAQGIHKLIRKHDLPGLMLRAF--DTLPEMIMTPHQAWQRQI 628

Query: 629 RGDVELVRIRDAEGRIAAEGALPYPPGVLCVVPGEVW---GGAVQRYFLALEEGVNLLPG 685
           +G+VE + +    GR++A   LPYPPGV  ++PGE+       V  + L L       PG
Sbjct: 629 KGEVETIALEQLVGRVSANMILPYPPGVPLLMPGEMLTKESRTVLDFLLMLCSVGQHYPG 688

Query: 686 FSPELQGVYSETDADGVKRL 705
           F  ++ G  ++ D DGV R+
Sbjct: 689 FETDIHG--AKQDEDGVYRV 706


Lambda     K      H
   0.322    0.138    0.420 

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: 1215
Number of extensions: 66
Number of successful extensions: 9
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: 711
Length of database: 713
Length adjustment: 39
Effective length of query: 672
Effective length of database: 674
Effective search space:   452928
Effective search space used:   452928
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 (21.9 bits)
S2: 55 (25.8 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 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