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 14332 b0186 lysine decarboxylase 2, constitutive (NCBI)

Query= BRENDA::P28629
         (755 letters)



>FitnessBrowser__Keio:14332
          Length = 713

 Score =  450 bits (1157), Expect = e-130
 Identities = 255/728 (35%), Positives = 389/728 (53%), Gaps = 48/728 (6%)

Query: 36  IKSTSFDDGFAILSSNEAIDCLMFSYQMEHP--------DEHQNVRQLIGKLHERQQNVP 87
           ++S     GF I+    ++D L F   +EH         D  +    L   +++  + +P
Sbjct: 22  LESALVAQGFQIIWPQNSVDLLKF---IEHNPRICGVIFDWDEYSLDLCSDINQLNEYLP 78

Query: 88  VFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTRYRQQLLPPLFSALM 147
           ++   +    +    +D+   +  F + L    D IA R       Y   + PP   AL 
Sbjct: 79  LYAFINTHSTMDVSVQDMRMALWFFEYALGQAED-IAIRMRQYTDEYLDNITPPFTKALF 137

Query: 148 KYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMGIERTSLGSLLDHTGAF 207
            Y    +Y++  PGH GG  + K+P G  ++D++G N  + D+ I  T LGSLLDHTG  
Sbjct: 138 TYVKERKYTFCTPGHMGGTAYQKSPVGCLFYDFFGGNTLKADVSISVTELGSLLDHTGPH 197

Query: 208 GESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVDRNCHKSIEQGLMLTGA 267
            E+E+Y AR FGA++S+ V  GTS SN+ +          +++DRNCHKS+   LM+   
Sbjct: 198 LEAEEYIARTFGAEQSYIVTNGTSTSNKIVGMYAAPSGSTLLIDRNCHKSLAHLLMMNDV 257

Query: 268 KPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKPSYCVVTNCTYDGVC 327
            PV++ P+RN  GI+G I  +E   +++++K++ +        Q P + V+TN TYDG+ 
Sbjct: 258 VPVWLKPTRNALGILGGIPRREFTRDSIEEKVAATT-----QAQWPVHAVITNSTYDGLL 312

Query: 328 YNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEPGDHNGPTVFATHSTHKL 387
           YN    +  L+  S  +HFD AW  Y  F+PIY     M GE     G  +F T STHK+
Sbjct: 313 YNTDWIKQTLDVPS--IHFDSAWVPYTHFHPIYQGKSGMSGERVA--GKVIFETQSTHKM 368

Query: 388 LNALSQASYIHVREGRGAINFSRFNQAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLT 447
           L ALSQAS IH++   G  +   FN+A+MMH TTSP Y I AS + A +M+ GN G  L 
Sbjct: 369 LAALSQASLIHIK---GEYDEEAFNEAFMMHTTTSPSYPIVASVETAAAMLRGNPGKRLI 425

Query: 448 QEVIDEAVDFRQAMARLYKEFTADGSWFFKPWNKEVVTDPQTGKTYDFADAPTKLLTTVQ 507
              ++ A+ FR+ + RL +E  +DG WFF  W    V + +                   
Sbjct: 426 NRSVERALHFRKEVQRLREE--SDG-WFFDIWQPPQVDEAE------------------- 463

Query: 508 DCWVMHPGESWHGFKDIPDNWSMLDPIKVSILAPGMGEDGELEETGVPAALVTAWLGRHG 567
            CW + PGE WHGF D   +   LDP+KV+IL PGM E G + E G+PAALV  +L   G
Sbjct: 464 -CWPVAPGEQWHGFNDADADHMFLDPVKVTILTPGMDEQGNMSEEGIPAALVAKFLDERG 522

Query: 568 IVPTRTTDFQIMFLFSMGVTRGKWGTLVNTLCSFKRHYDANTPLAQVMPELVEQYPDTYA 627
           IV  +T  + ++FLFS+G+ + K   L+  L  FKR YD N  +  ++P+L  + PD Y 
Sbjct: 523 IVVEKTGPYNLLFLFSIGIDKTKAMGLLRGLTEFKRSYDLNLRIKNMLPDLYAEDPDFYR 582

Query: 628 NMGIHDLGDTMFAWLKENNPGARLNEAYSGLPVAEVTPREAYNAIVDNNVELVSIENLPG 687
           NM I DL   +   +++++    +  A+  LP   +TP +A+   +   VE +++E L G
Sbjct: 583 NMRIQDLAQGIHKLIRKHDLPGLMLRAFDTLPEMIMTPHQAWQRQIKGEVETIALEQLVG 642

Query: 688 RIAANSVIPYPPGIPMLLSGENFGDKNSPQVSYLRSLQSWDHHFPGFEHETEGT-EIIDG 746
           R++AN ++PYPPG+P+L+ GE    ++   + +L  L S   H+PGFE +  G  +  DG
Sbjct: 643 RVSANMILPYPPGVPLLMPGEMLTKESRTVLDFLLMLCSVGQHYPGFETDIHGAKQDEDG 702

Query: 747 IYHVMCVK 754
           +Y V  +K
Sbjct: 703 VYRVRVLK 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: 1393
Number of extensions: 78
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: 713
Length adjustment: 40
Effective length of query: 715
Effective length of database: 673
Effective search space:   481195
Effective search space used:   481195
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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