Alignments for a candidate for adiA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Acidovorax sp. GW101-3H11

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate Ac3H11_2914 Arginine decarboxylase (EC 4.1.1.19); Ornithine decarboxylase (EC 4.1.1.17); Lysine decarboxylase (EC 4.1.1.18)

Query= BRENDA::E8X9U7
         (756 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2914
          Length = 761

 Score =  515 bits (1327), Expect = e-150
 Identities = 281/751 (37%), Positives = 422/751 (56%), Gaps = 31/751 (4%)

Query: 4   VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQ 63
           ++I++ ++  ++T  G  +  LA A+  +   V+  TS+ D              + S  
Sbjct: 7   IIIIDEDYRSENT-SGLGIRALAQAIETEGFEVVGVTSYGDLSQFAQQQSRASAFILSID 65

Query: 64  MEQ-------PDEHLSVRQLIGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFAWI 116
            E+           LS+R  IG++  +  +VP+++ G+  K +  L  D+L  +  F  +
Sbjct: 66  DEEFTVGEGLDPIVLSLRNFIGEVRRKNADVPIYVHGET-KTSRHLPNDILRELHGFIHM 124

Query: 117 LEDTADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGR 176
            EDT +F+A   +     Y + + PP F AL+ Y++   YSW  PGH GGV F K+P G+
Sbjct: 125 FEDTPEFVARHIIREAKSYLESVQPPFFKALLDYAEDGSYSWHCPGHSGGVAFLKSPVGQ 184

Query: 177 FYHDYYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNR 236
            YH +YGEN+ R+D+      LG LLDH GA GESE+NAAR+F AD  + V  GTS SN+
Sbjct: 185 MYHQFYGENMLRADVCNAVEELGQLLDHNGAIGESERNAARIFNADHCFFVTNGTSTSNK 244

Query: 237 TIMQACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETL 296
            +    +   DVVV+DRNCHKSI   +I+TGA PV+M P+RN +GIIGPI   E +P  +
Sbjct: 245 MVWHHTVAPGDVVVVDRNCHKSILHSIIMTGAIPVFMKPTRNHFGIIGPIPQSEFEPAAI 304

Query: 297 QKKISASPLTKTKAGQ--KPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGY 354
           Q KI A+PL K    +  KP    +T  TYDGV YN +  + +L    D +HFDEAW  +
Sbjct: 305 QAKIKANPLLKGVDAKKVKPRVLTLTQSTYDGVLYNTETIKGMLDGYVDNLHFDEAWLPH 364

Query: 355 ARFNPIYCDHYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRGA-VNFSRFN 413
           A F+P Y  ++AM  +         +AT S HKLL  +SQAS++ V++ + A ++   FN
Sbjct: 365 AAFHPFYGSYHAMGKKRTRPKYSVTYATQSIHKLLAGISQASHVLVQDSQTAKLDRHLFN 424

Query: 414 QAYMMHATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEG 473
           +AY+MH +TSP Y+I AS DVA +MM+   G +L +E + EA+DFR+AM ++ ++F  + 
Sbjct: 425 EAYLMHTSTSPQYSIIASCDVAAAMMEPPGGTALVEESLLEALDFRRAMRQVEEDF-GKN 483

Query: 474 DWFFKPWNKDVVTDPQTGKTYDF---ADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWS 530
           DW+FK W  D + D   G+  D+   +D   K           + G  WHGF  L D ++
Sbjct: 484 DWWFKVWGPDKLVDEGLGRAEDWIIRSDGKGK-----------KNGSKWHGFGQLADGFN 532

Query: 531 MLDPIKVSILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRG 590
           MLDPIK +I+ PG+  DG+ + +G+PA++VT +L  HG+V  +T  +    +F++G+T+G
Sbjct: 533 MLDPIKSTIVTPGLNLDGKFDKTGIPASIVTKYLAEHGVVVEKTGLYSFFIMFTIGITKG 592

Query: 591 KWGTLINTLCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGA 650
           +W TL+  L  FK  Y+ N P+ +++PE  Q +   Y  MG+ DL   +     + +   
Sbjct: 593 RWNTLLTALQQFKDDYEKNQPMWRILPEFCQQH-KRYERMGLRDLCQHVHEMYAKYDIAR 651

Query: 651 RLNAAYSTLPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGEN 710
                Y +     + P DAY  I +   E V I+NL GRI    V PYPPGIP+L+ GE 
Sbjct: 652 LTTEMYLSDLTPAMKPSDAYAHIAHRTTERVEIDNLEGRITVGLVTPYPPGIPLLIPGEV 711

Query: 711 FGDENSPQVGYLRSLQSWDHHFPGFEHETEG 741
           F   N   V YL+  + +    PGFE +  G
Sbjct: 712 F---NKKIVDYLKFAREFAKLCPGFETDIHG 739


Lambda     K      H
   0.319    0.135    0.415 

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: 1484
Number of extensions: 84
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: 756
Length of database: 761
Length adjustment: 40
Effective length of query: 716
Effective length of database: 721
Effective search space:   516236
Effective search space used:   516236
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.

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