GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Pseudomonas fluorescens FW300-N1B4

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate Pf1N1B4_4600 Lysine decarboxylase, inducible (EC 4.1.1.18)

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4600
          Length = 751

 Score =  379 bits (974), Expect = e-109
 Identities = 224/627 (35%), Positives = 337/627 (53%), Gaps = 29/627 (4%)

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

Query: 173 IFRSDICNADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAP 232
             RSD+  +  +LG LL H GP  +AE  AAR F AD T+FV+NGT+T+N I   + VA 
Sbjct: 194 TLRSDLSVSVPELGSLLDHTGPLAEAEARAARNFGADHTFFVINGTSTANKIVWHSMVAR 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 LTKGREPK-VKLAVVTNSTYDGLCYNAELIKQSLGNSVEVLHFDEAWYAYAAFHEFFAGR 371

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

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

Query: 466 PPVVHGKPWQDADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDVE 525
           PP   G        E++V+  + W  +  A WHGF G  D+   +DP K  L  PG+   
Sbjct: 488 PPSAEG-------IEQVVT--EDWLLQPDADWHGFGGVTDDYVLLDPIKVTLVMPGL-TA 537

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

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

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

Query: 703 LEESINRFPGFAPEIQGVYFEKE-NGK 728
                + FPGF  ++ G+  E E NG+
Sbjct: 716 ARTFDSSFPGFVADVHGLQHEDEGNGR 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: 1134
Number of extensions: 55
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 (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