Aligments for a candidate for odc in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Keio:18145 b4117 biodegradative arginine
           decarboxylase (RefSeq)
          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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources