Alignments for a candidate for cadA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Escherichia coli BW25113

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate 18145 b4117 biodegradative arginine decarboxylase (RefSeq)

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__Keio:18145
          Length = 755

 Score =  568 bits (1463), Expect = e-166
 Identities = 307/762 (40%), Positives = 443/762 (58%), Gaps = 30/762 (3%)

Query: 9   VLIVHRD-IKADTVAGERVRGIAHELEQDGFSILSTASSAEGRIVASTHHGLACILVAAE 67
           VLIV  + +  DT  G  V  +A  L Q   +++ + S  +G  + S++  + C++ + +
Sbjct: 3   VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQ 62

Query: 68  GAGENQRLLQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRG-ILYLFE 126
               ++   Q+V +LI     R   +P+F LG++   E A A    DL +L     ++ E
Sbjct: 63  MEHPDEH--QNVRQLIGKLHERQQNVPVFLLGDR---EKALAAMDRDLLELVDEFAWILE 117

Query: 127 DTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAF 186
           DT  F+A +   A   Y   LLPP F AL++++    YSW  PGH GGV + K+P G+ +
Sbjct: 118 DTADFIAGRAVAAMTRYRQQLLPPLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFY 177

Query: 187 HQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKIV 246
           H ++GEN  R+D+ +    LGSLLDHTG   E+E  AAR FGAD ++ V+ GTS +N+ +
Sbjct: 178 HDYYGENLFRTDMGIERTSLGSLLDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTI 237

Query: 247 WHSMVGREDLVLVDRNCHKSILHSIIMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAA 306
             + +   D+V+VDRNCHKSI   +++TGA P+Y+ P RN  GIIGPI   E   +++  
Sbjct: 238 MQACMTDNDVVVVDRNCHKSIEQGLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQK 297

Query: 307 KIAASPLARGRE-PKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFH 365
           KI+ SPL + +   K    VVTN TYDG+CYNA+  +  L  + + LHFDEAWY YA F+
Sbjct: 298 KISESPLTKDKAGQKPSYCVVTNCTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFN 357

Query: 366 EFYDGRYGM-GTSRSEEGPLVFATHSTHKMLAAFSQASMIHVQDGGTRKLDVARFNEAFM 424
             Y   Y M G      GP VFATHSTHK+L A SQAS IHV++G    ++ +RFN+A+M
Sbjct: 358 PIYADHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREG-RGAINFSRFNQAYM 416

Query: 425 MHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRN-DWWF 483
           MH +TSP Y I AS DVA +MM+G +G SL QE  DEA+ FR+A+A + +    +  W+F
Sbjct: 417 MHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFF 476

Query: 484 GVWQPEQVEGTDQVGTHD---------------WVLEPSADWHGFGDIAEDYVLLDPIKV 528
             W  E V       T+D               WV+ P   WHGF DI +++ +LDPIKV
Sbjct: 477 KPWNKEVVTDPQTGKTYDFADAPTKLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKV 536

Query: 529 TLTTPGLSAGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVT 588
           ++  PG+   G+L E G+PAA+V+ +L   G+V  +T  +  + LFSMG+T+GKW TLV 
Sbjct: 537 SILAPGMGEDGELEETGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVN 596

Query: 589 ELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMYT 648
            L  FKR YDAN PL  V+P + +     Y  +G+ DL D M A  ++N     +   Y+
Sbjct: 597 TLCSFKRHYDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAYS 656

Query: 649 VLPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRS 708
            LP   + P EAY+ +V   VE V I  L GRIAA  ++PYPPGIP+++ GE F +    
Sbjct: 657 GLPVAEVTPREAYNAIVDNNVELVSIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSP 716

Query: 709 ILDYLEFARTFERAFPGFDSDVHGLQHQDGPSGRCYTVECIK 750
            + YL   ++++  FPGF+ +  G +  DG     Y V C+K
Sbjct: 717 QVSYLRSLQSWDHHFPGFEHETEGTEIIDG----IYHVMCVK 754


Lambda     K      H
   0.320    0.136    0.407 

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: 1418
Number of extensions: 75
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: 751
Length of database: 755
Length adjustment: 40
Effective length of query: 711
Effective length of database: 715
Effective search space:   508365
Effective search space used:   508365
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 (21.8 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