Alignments for a candidate for adiA in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for adiA in Pseudomonas benzenivorans DSM 8628

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate WP_090444202.1 BLS63_RS11675 arginine decarboxylase

Query= BRENDA::E8X9U7
         (756 letters)



>NCBI__GCF_900100495.1:WP_090444202.1
          Length = 766

 Score =  811 bits (2094), Expect = 0.0
 Identities = 385/757 (50%), Positives = 526/757 (69%), Gaps = 6/757 (0%)

Query: 3   KVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSY 62
           +VL+V+ +        G  +  L +   ++N  VIK+ SF+DG A + A+ A+ C+   +
Sbjct: 12  RVLLVDDDLAQPTGARGRVLNELVEEFHERNTEVIKAASFEDGMASVVADAALHCICVDW 71

Query: 63  QMEQPD--EHLSVRQLIGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFAWILEDT 120
            +   D   H+   +L+  + +R + VPVFL+ DR+ A  S+  + +EL DEF W+LEDT
Sbjct: 72  TLGSNDAASHVLALELLRAIRQRHEQVPVFLMADRD-AKRSITVEAMELADEFIWMLEDT 130

Query: 121 ADFIAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHD 180
           A F+AGR +AA+ RY + LLPP  +AL++Y+   E+SWAAPGHQGG+ FTK+P GR + D
Sbjct: 131 APFVAGRVIAAIERYLEHLLPPFTDALIRYTLKDEHSWAAPGHQGGIAFTKSPIGRVFFD 190

Query: 181 YYGENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTIMQ 240
           ++GENLFR+D GIER  LGS+LDH+G  GESE  AAR+FGA  S++V+ GTSGSNR I  
Sbjct: 191 FFGENLFRADSGIERGNLGSVLDHSGPVGESEAYAARIFGAHVSYAVLNGTSGSNRAIFM 250

Query: 241 ACMTDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKI 300
           AC+ +N   + DRNCHKSIEQGL+L+G  PVYM P+RNR+GIIGPI P++   + +   I
Sbjct: 251 ACVGENQFALCDRNCHKSIEQGLVLSGGLPVYMTPTRNRFGIIGPILPEQFDQQRIAAAI 310

Query: 301 SASPLTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFNPI 360
           ++ PL     G +  Y+VVTNCTYDG+C +A+ A+ LLA++SDRIHFDEAWYGYARFNP+
Sbjct: 311 ASHPLRAQAKGDQAVYAVVTNCTYDGMCLDAERAEGLLAQSSDRIHFDEAWYGYARFNPL 370

Query: 361 YCDHYAMRGEPGDH--NGPTVFATHSTHKLLNALSQASYIHVREGRGAVNFSRFNQAYMM 418
           Y    AMRG+P +H  + PTVFATHSTHKLL ALSQ+SYIH+R GR  +  SRFN+++++
Sbjct: 371 YRGRLAMRGDPAEHKADAPTVFATHSTHKLLAALSQSSYIHIRNGRNPIEHSRFNESFVI 430

Query: 419 HATTSPLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEFTDEGDWFFK 478
            A+TSPLYA+ ASN++  +MMDGN G SLTQ+ I EAVDFRQA+AR+++EF   GDWFF+
Sbjct: 431 QASTSPLYAMFASNEIGAAMMDGNGGYSLTQDAIREAVDFRQALARVHREFASRGDWFFQ 490

Query: 479 PWNKDVVTDPQTGKTYDFADAPAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLDPIKVS 538
           PWN   V D ++GK  DFADA A+ L +D  CW + PG  WHGF  L   W +LDPIKV 
Sbjct: 491 PWNAPQVRD-RSGKLVDFADAEAEQLGSDPACWELEPGAEWHGFAGLEKGWCLLDPIKVG 549

Query: 539 ILAPGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLINT 598
           I+ PGMG DG+LEA G+PA ++ A+L R+ IVP+R TDF ++ LFS+GVT+GKW TLIN 
Sbjct: 550 IMVPGMGGDGQLEAEGIPAPVLGAFLYRNNIVPSRITDFMVLCLFSIGVTKGKWATLINV 609

Query: 599 LCSFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLNAAYST 658
           L +FK HYD N  L +++P+LV  +P+ Y  MG+ DL  +MF  +R +   A    A+  
Sbjct: 610 LLAFKRHYDNNVALERLLPDLVAQHPERYRGMGLRDLSREMFEHMRNSRMDALQAQAFGQ 669

Query: 659 LPVAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGDENSPQ 718
           LP  E+TPR A+ A+     E++ ++    R+    V+PYPPGIP+++ GEN G  + P 
Sbjct: 670 LPQIEMTPRGAFQALQAGAAELLPLKQAAKRVTGVGVMPYPPGIPIVMPGENLGALDGPW 729

Query: 719 VGYLRSLQSWDHHFPGFEHETEGTEIIDGVYHVMCVK 755
           + Y+ +LQ W + FPGFE E  G E  DG YH  C+K
Sbjct: 730 LSYILALQDWGNRFPGFEKEVSGAEHKDGGYHFWCLK 766


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: 1565
Number of extensions: 83
Number of successful extensions: 5
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: 766
Length adjustment: 40
Effective length of query: 716
Effective length of database: 726
Effective search space:   519816
Effective search space used:   519816
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 24 2021. The underlying query database was built on Sep 17 2021.

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

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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