GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Klebsiella michiganensis M5al

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate BWI76_RS07195 BWI76_RS07195 lysine decarboxylase CadA

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__Koxy:BWI76_RS07195
          Length = 715

 Score =  335 bits (860), Expect = 4e-96
 Identities = 211/620 (34%), Positives = 321/620 (51%), Gaps = 32/620 (5%)

Query: 114 EIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENI 173
           +I+    +Y D +LPP  KAL  YV  G   F  PGH GG  F+KSP G  FY+F+G N 
Sbjct: 116 KIKQNTDEYIDTILPPLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSIFYDFFGSNT 175

Query: 174 FRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPG 233
            +SDI  +  +LG LL H GP  +AE++ ARVFNA+++Y V NGT+T+N I    +   G
Sbjct: 176 MKSDISISVSELGSLLDHSGPHKEAEEYIARVFNAERSYMVTNGTSTANKIVGMYSAPAG 235

Query: 234 DLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDP 293
             VL DRN HKS+ +  ++ +   P+Y   +R++YG +GGI   +F   +I +++     
Sbjct: 236 STVLIDRNCHKSLTH-LMMMSDITPIYFRPTRNAYGILGGIPQSEFQHATIAKRV----K 290

Query: 294 EKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSS 353
           E   A  P   AVI   TYDG +YN   + + +      I FDSAWV Y  F P+ +   
Sbjct: 291 ETPNATWPVH-AVITNSTYDGLLYNTDYIKKTLD--VKSIHFDSAWVPYTNFSPIYEGKC 347

Query: 354 PLLLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSS 413
             +     +   I  TQSTHK  A FSQAS I     H+KG    +N + FN AYM  ++
Sbjct: 348 G-MSGGRVEGKVIYETQSTHKLLAAFSQASMI-----HVKGD---VNEETFNEAYMMHTT 398

Query: 414 TSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLKNATMIKPFLPPVVHGKP 473
           TSP Y + A+ +  A M +G AGK+L   ++  S+  RK + +       +   V     
Sbjct: 399 TSPHYGVVASTETAAAMMKGNAGKRLIDGSIERSIKFRKEIKRLKGESDGWFFDV----- 453

Query: 474 WQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVETGEYEDFG 533
           WQ     + +   + W     + WHGF    +   ++DP K  L TPG+  + G  +DFG
Sbjct: 454 WQ----PEHIDGAECWPLRSDSAWHGFKNIDNEHMYLDPIKVTLLTPGMK-KDGTMDDFG 508

Query: 534 IPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLVKADAPLDE 593
           IPA I+A YL EHGI+ EK    ++LFL +    + K  +L+  +  F+     +  +  
Sbjct: 509 IPASIVAKYLDEHGIVVEKTGPYNLLFLFSIGIDKTKALSLLRALTDFKRAFDLNLRVKN 568

Query: 594 VLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAMTPYQANVE 653
           +LP LY E  + YE   +++L Q +H   +++N  +     F  +  P   +TPY A  +
Sbjct: 569 MLPSLYREDPEFYENMRVQELAQNIHKLIEHHNLPDLMFRAF--EVLPTMMITPYAAFQK 626

Query: 654 LLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQ---KYFLILEESINRF 710
            L    + V L ++ G       LPYPPG+  ++PGE  T+ ++   ++  +L E    +
Sbjct: 627 ELHGQTEEVYLEEMVGRVNANMILPYPPGVPLVMPGEMITEESRPVLEFLQMLCEIGAHY 686

Query: 711 PGFAPEIQGVYFEKENGKSV 730
           PGF  +I G Y + +   +V
Sbjct: 687 PGFETDIHGAYRQADGRYTV 706


Lambda     K      H
   0.318    0.136    0.405 

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: 1298
Number of extensions: 73
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: 745
Length of database: 715
Length adjustment: 40
Effective length of query: 705
Effective length of database: 675
Effective search space:   475875
Effective search space used:   475875
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: 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