GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:14332
          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:

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