GapMind for catabolism of small carbon sources

 

Aligments for a candidate for odc in Pseudomonas fluorescens FW300-N2E3

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate AO353_23560 AO353_23560 lysine decarboxylase

Query= BRENDA::Q5ZH57
         (745 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_23560 AO353_23560 lysine
           decarboxylase
          Length = 751

 Score =  378 bits (971), Expect = e-109
 Identities = 223/627 (35%), Positives = 337/627 (53%), Gaps = 29/627 (4%)

Query: 113 REIEAAAKKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGEN 172
           R++  AA+ Y DG+LPPFFKAL  +    N  +  PGH GG  + KSP G+ F+ F+GEN
Sbjct: 134 RQVARAARSYLDGLLPPFFKALVQHTADSNYSWHTPGHGGGVAYHKSPVGQAFHQFFGEN 193

Query: 173 IFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAP 232
             RSD+  +  +LG LL H GP  +AE  AAR F AD T+FV+NGT+T+N I   A VA 
Sbjct: 194 TLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTSTANKIVWQAMVAR 253

Query: 233 GDLVLFDRNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVD 292
            DLVL DRN HKSV + +++  G  P+YL   R+  G IG I   +F  +SI+ KI    
Sbjct: 254 DDLVLVDRNCHKSVLH-SIIMTGAIPLYLCPERNELGIIGPIPLSEFSRESIQAKIDASP 312

Query: 293 PEKAKAKRPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDS 352
             K +  +  +LAV+   TYDG  YNA+ + + +G+  + + FD AW  Y  F       
Sbjct: 313 LTKGRTPK-VKLAVVTNSTYDGLCYNAELIKQTLGNSVEVLHFDEAWYAYAAFHEFFAGR 371

Query: 353 SPLLLNLGPDDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFS 412
             +  +   D P +  T STHK  A FSQAS IH +D    G  R ++  +FN A+M   
Sbjct: 372 YGMGTSRTDDSPLVFTTHSTHKLLAAFSQASMIHVQD----GGARQLDRDRFNEAFMMHI 427

Query: 413 STSPFYPLFATLDINAKMQEGEAGKKLWHDALVTSV-------NARKNLLKNATMIKPFL 465
           STSP Y + A+LD+ + M EG AG+ L  +    ++       N R+++  +      + 
Sbjct: 428 STSPQYSIIASLDVASAMMEGPAGRSLLQEMFDEALSFRRALANLRQHIATDDWWFSIWQ 487

Query: 466 PPVVHGKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVE 525
           PP+V G        +K+ +    W  +  A WHGF   A++   +DP K  L  PG+   
Sbjct: 488 PPLVEG-------IDKVTT--SDWLLQPEADWHGFGDIAEDYVLLDPIKVTLVMPGL-TA 537

Query: 526 TGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESLV 585
            G   + GIPA +++ +L E G++ EK  L S L L +   T+ K   L+T++++F+   
Sbjct: 538 GGALSERGIPAAVVSKFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLLTELLEFKRSY 597

Query: 586 KADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQAM 645
            A+  L   LP +      RY+G  ++ LC ++H  Y++N T ++ K M+     PE AM
Sbjct: 598 DANVSLATCLPCVAQRDVARYQGMGLRDLCDQLHACYRSNATAKHLKRMY--TVLPEIAM 655

Query: 646 TPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKWTKVAQK---YFLI 702
            P  A  +L++   + V + +++G  A    +PYPPGI  I+PGE++T+  +    Y   
Sbjct: 656 KPADAYDQLVRGEVEAVSIDNLQGRIAAVMLVPYPPGIPLIMPGERFTESTRSIIDYLAF 715

Query: 703 LEESINRFPGFAPEIQGVYFEKE-NGK 728
                + FPGF  ++ G+  E E NG+
Sbjct: 716 ARTFNSSFPGFVADVHGLQHEDEGNGR 742


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: 1102
Number of extensions: 46
Number of successful extensions: 8
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: 751
Length adjustment: 40
Effective length of query: 705
Effective length of database: 711
Effective search space:   501255
Effective search space used:   501255
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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