Alignments for a candidate for adiA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Escherichia coli BW25113

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate 18159 b4131 lysine decarboxylase 1 (NCBI)

Query= BRENDA::P28629
         (755 letters)



>FitnessBrowser__Keio:18159
          Length = 715

 Score =  465 bits (1196), Expect = e-135
 Identities = 261/737 (35%), Positives = 397/737 (53%), Gaps = 48/737 (6%)

Query: 21  VERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLH 80
           +  L  AL + N  ++     DD   ++ +N  +  ++F +   +        +L  ++ 
Sbjct: 19  IRELHRALERLNFQIVYPNDRDDLLKLIENNARLCGVIFDWDKYN-------LELCEEIS 71

Query: 81  ERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTRYRQQLLP 140
           +  +N+P++   +    L     DL   +  F + L   A+ IA +       Y   +LP
Sbjct: 72  KMNENLPLYAFANTYSTLDVSLNDLRLQISFFEYAL-GAAEDIANKIKQTTDEYINTILP 130

Query: 141 PLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMGIERTSLGSL 200
           PL  AL KY    +Y++  PGH GG  F K+P G  ++D++G N  ++D+ I  + LGSL
Sbjct: 131 PLTKALFKYVREGKYTFCTPGHMGGTAFQKSPVGSLFYDFFGPNTMKSDISISVSELGSL 190

Query: 201 LDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVDRNCHKSIEQ 260
           LDH+G   E+E+Y ARVF ADRS+ V  GTS +N+ +          +++DRNCHKS+  
Sbjct: 191 LDHSGPHKEAEQYIARVFNADRSYMVTNGTSTANKIVGMYSAPAGSTILIDRNCHKSLTH 250

Query: 261 GLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKPSYCVVTN 320
            +M++   P+Y  P+RN YGI+G I   E Q  T+ K++ E+P         P + V+TN
Sbjct: 251 LMMMSDVTPIYFRPTRNAYGILGGIPQSEFQHATIAKRVKETP-----NATWPVHAVITN 305

Query: 321 CTYDGVCYNAKEAQDLLEKTSD--RLHFDEAWYGYARFNPIYADHYAMRGEPGDHNGPTV 378
            TYDG+ YN     D ++KT D   +HFD AW  Y  F+PIY     M G  G   G  +
Sbjct: 306 STYDGLLYNT----DFIKKTLDVKSIHFDSAWVPYTNFSPIYEGKCGMSG--GRVEGKVI 359

Query: 379 FATHSTHKLLNALSQASYIHVREGRGAINFSRFNQAYMMHATTSPLYAICASNDVAVSMM 438
           + T STHKLL A SQAS IHV+   G +N   FN+AYMMH TTSP Y I AS + A +MM
Sbjct: 360 YETQSTHKLLAAFSQASMIHVK---GDVNEETFNEAYMMHTTTSPHYGIVASTETAAAMM 416

Query: 439 DGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFFKPWNKEVVTDPQTGKTYDFADA 498
            GN+G  L    I+ A+ FR+ + RL  E  +DG WFF  W                   
Sbjct: 417 KGNAGKRLINGSIERAIKFRKEIKRLRTE--SDG-WFFDVWQ------------------ 455

Query: 499 PTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKVSILAPGMGEDGELEETGVPAAL 558
           P  + TT  +CW +    +WHGFK+I +    LDPIKV++L PGM +DG + + G+PA++
Sbjct: 456 PDHIDTT--ECWPLRSDSTWHGFKNIDNEHMYLDPIKVTLLTPGMEKDGTMSDFGIPASI 513

Query: 559 VTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVNTLCSFKRHYDANTPLAQVMPEL 618
           V  +L  HGIV  +T  + ++FLFS+G+ + K  +L+  L  FKR +D N  +  ++P L
Sbjct: 514 VAKYLDEHGIVVEKTGPYNLLFLFSIGIDKTKALSLLRALTDFKRAFDLNLRVKNMLPSL 573

Query: 619 VEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAYSGLPVAEVTPREAYNAIVDNNVE 678
             + P+ Y NM I +L   +   +  +N    +  A+  LP   +TP  A+   +    E
Sbjct: 574 YREDPEFYENMRIQELAQNIHKLIVHHNLPDLMYRAFEVLPTMVMTPYAAFQKELHGMTE 633

Query: 679 LVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSPQVSYLRSLQSWDHHFPGFEHET 738
            V ++ + GRI AN ++PYPPG+P+++ GE   +++ P + +L+ L     H+PGFE + 
Sbjct: 634 EVYLDEMVGRINANMILPYPPGVPLVMPGEMITEESRPVLEFLQMLCEIGAHYPGFETDI 693

Query: 739 EGT-EIIDGIYHVMCVK 754
            G     DG Y V  +K
Sbjct: 694 HGAYRQADGRYTVKVLK 710


Lambda     K      H
   0.319    0.135    0.414 

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: 1360
Number of extensions: 83
Number of successful extensions: 6
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: 755
Length of database: 715
Length adjustment: 40
Effective length of query: 715
Effective length of database: 675
Effective search space:   482625
Effective search space used:   482625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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