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 18145 b4117 biodegradative arginine decarboxylase (RefSeq)

Query= BRENDA::Q5ZH57
         (745 letters)



>FitnessBrowser__Keio:18145
          Length = 755

 Score =  358 bits (919), Expect = e-103
 Identities = 221/678 (32%), Positives = 342/678 (50%), Gaps = 31/678 (4%)

Query: 63  KAIINKADETKFNIPIFIITDDSSKVDGETMSKIFHIID---WHNNYDRRLYDREIEAAA 119
           + +I K  E + N+P+F++  D  K        +  ++D   W              AA 
Sbjct: 73  RQLIGKLHERQQNVPVFLL-GDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAM 131

Query: 120 KKYEDGVLPPFFKALKAYVERGNIQFDCPGHQGGQYFRKSPAGREFYNFYGENIFRSDIC 179
            +Y   +LPP F AL  Y +     +  PGHQGG  F K+PAGR ++++YGEN+FR+D+ 
Sbjct: 132 TRYRQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMG 191

Query: 180 NADVDLGDLLIHEGPAMDAEKHAARVFNADKTYFVMNGTTTSNNIAITAAVAPGDLVLFD 239
                LG LL H G   ++EK+AARVF AD+++ V+ GT+ SN   + A +   D+V+ D
Sbjct: 192 IERTSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVD 251

Query: 240 RNNHKSVYNAALVQAGGRPVYLETSRDSYGFIGGIYSKDFDEKSIREKIAKVDPEKAKAK 299
           RN HKS+    L+  G +PVY+  SR+ YG IG IY ++   +++++KI++    K KA 
Sbjct: 252 RNCHKSI-EQGLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAG 310

Query: 300 RPFRLAVIQLGTYDGTIYNAKQVVERIGHLCDYILFDSAWVGYEQFIPMMKDSSPLLLNL 359
           +     V+   TYDG  YNAK+  + +    D + FD AW GY +F P+  D   +    
Sbjct: 311 QKPSYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEP 370

Query: 360 GP-DDPGILVTQSTHKQQAGFSQASQIHKKDSHIKGQKRYINHKQFNNAYMKFSSTSPFY 418
           G  + P +  T STHK     SQAS IH ++      +  IN  +FN AYM  ++TSP Y
Sbjct: 371 GDHNGPTVFATHSTHKLLNALSQASYIHVREG-----RGAINFSRFNQAYMMHATTSPLY 425

Query: 419 PLFATLDINAKMQEGEAGKKLWHDALVTSVNARKNLLK--------NATMIKPFLPPVV- 469
            + A+ D+   M +G +G  L  + +  +V+ R+ + +         +   KP+   VV 
Sbjct: 426 AICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFFKPWNKEVVT 485

Query: 470 ---HGKPWQ--DADTEKIVSDIDYWKFEKGAKWHGFDGYADNQYFVDPNKFMLTTPGIDV 524
               GK +   DA T+ + +  D W    G  WHGF    DN   +DP K  +  PG+  
Sbjct: 486 DPQTGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKVSILAPGMG- 544

Query: 525 ETGEYEDFGIPAVILANYLREHGIIPEKNDLNSILFLMTPAETQAKMDNLVTQIVKFESL 584
           E GE E+ G+PA ++  +L  HGI+P +     I+FL +   T+ K   LV  +  F+  
Sbjct: 545 EDGELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVNTLCSFKRH 604

Query: 585 VKADAPLDEVLPRLYSEHQDRYEGYTIKQLCQEVHDFYKNNNTKEYQKEMFLGKYFPEQA 644
             A+ PL +V+P L  ++ D Y    I  L   +  + K NN      E + G   P   
Sbjct: 605 YDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAYSG--LPVAE 662

Query: 645 MTPYQANVELLKNNAKLVPLTDIEGLAALEGALPYPPGIFCIVPGEKW---TKVAQKYFL 701
           +TP +A   ++ NN +LV + ++ G  A    +PYPPGI  ++ GE +         Y  
Sbjct: 663 VTPREAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSPQVSYLR 722

Query: 702 ILEESINRFPGFAPEIQG 719
            L+   + FPGF  E +G
Sbjct: 723 SLQSWDHHFPGFEHETEG 740


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: 1248
Number of extensions: 58
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: 755
Length adjustment: 40
Effective length of query: 705
Effective length of database: 715
Effective search space:   504075
Effective search space used:   504075
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