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_090444206.1 BLS63_RS11680 arginine decarboxylase

Query= BRENDA::E8X9U7
         (756 letters)



>NCBI__GCF_900100495.1:WP_090444206.1
          Length = 766

 Score =  600 bits (1548), Expect = e-176
 Identities = 318/744 (42%), Positives = 452/744 (60%), Gaps = 15/744 (2%)

Query: 4   VLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGYAILSANEAIDCLMFSYQ 63
           VLIV      +D+ V +  + +  AL    + V    S +D      A+ A  C++  + 
Sbjct: 18  VLIVLDIRGSEDSIVTHRAQEIGRALQAHEIEVEMVGSLEDAEIAFRADPAYSCVILGWG 77

Query: 64  MEQPDEHLSVRQLIGKLHERQQNVPVFLLGDREKATASLDRDLLELVDEFAWILEDTADF 123
           + + D   ++ Q+I  +  R   +P+ +LG  +   + +    LE +D F W  ED+ +F
Sbjct: 78  LCEHDLDKAL-QVIRLIRRRTAQLPI-ILGMSQAHQSRVPLAFLENIDGFIWQPEDSPEF 135

Query: 124 IAGRAVAAMTRYRQQLLPPLFNALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYG 183
           IAGR  AA  RY   +LPP F AL+ ++D  EYSW  PGH GG  F KT  GR + D+YG
Sbjct: 136 IAGRIQAAARRYLDTILPPFFGALVNFADTCEYSWHTPGHTGGTAFMKTAVGRSFLDFYG 195

Query: 184 ENLFRSDMGIERTTLGSLLDHTGAFGESEKNAARVFGADRSWSVVVGTSGSNRTIMQACM 243
           E + RSD+ +    LGSL DH+G   E+EK AARVFGAD S+  V G+S SN+ ++ + +
Sbjct: 196 EQMLRSDLSVSVGQLGSLNDHSGPVAEAEKYAARVFGADYSFFSVGGSSASNQMVLHSAV 255

Query: 244 TDNDVVVLDRNCHKSIEQGLILTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISAS 303
           TD D V++DRNCHKS+   L  +GA P+Y+ P RN  G+IGP+   E+ PE + +K++ S
Sbjct: 256 TDGDAVLVDRNCHKSLNYALNQSGAVPLYLRPRRNARGLIGPVPQSELTPEAVAQKLADS 315

Query: 304 PLTKTKAGQKPSYSVVTNCTYDGVCYNAKEAQDLLAKTSDRIHFDEAWYGYARFNPIYCD 363
           PL + K   +P  +V+TN TYDG+CYN +     L+++ DRIH+DEAWY YARFNP+Y  
Sbjct: 316 PLARDKQA-RPVLAVLTNSTYDGLCYNVQTTTRELSRSVDRIHYDEAWYAYARFNPLYEG 374

Query: 364 HYAMRGEPGDHNGPTVFATHSTHKLLNALSQASYIHVREGRGAVNFSRFNQAYMMHATTS 423
            Y M       +  TV  THSTHKLL ALSQAS IH+R G+  V  + FN+A+MMH +TS
Sbjct: 375 RYGMHRGERHADDATVTVTHSTHKLLAALSQASMIHIRSGKVPVKPALFNEAFMMHTSTS 434

Query: 424 PLYAICASNDVAVSMMDGNSGLSLTQEVIDEAVDFRQAMARLYKEF--TDEGDWFFKPWN 481
           P Y+I AS DV+  MMD ++G  LT E I EA+ FRQAM R+  E    D  DW+F  W 
Sbjct: 435 PQYSIIASTDVSTKMMD-DAGEYLTDESIGEAIAFRQAMVRMSNEIHIRDPKDWWFGVWQ 493

Query: 482 KDVVTDPQTGKTYDFADA-PAKLLATDQNCWVMRPGETWHGFKDLPDNWSMLDPIKVSIL 540
            D V          FAD  P +L   D   WV++P   WHGF DL  ++ MLDPIKV++L
Sbjct: 494 PDEVDG------VPFADLEPQRLHHGD--AWVLKPNARWHGFGDLGPDYCMLDPIKVTVL 545

Query: 541 APGMGDDGELEASGVPAALVTAWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLINTLC 600
            PG   +GE+++SG+PA LV+++L   GIV  +T  + I+ LFS+GVT+GKWG+L   L 
Sbjct: 546 TPGQTLEGEMQSSGIPAPLVSSFLSSRGIVVEKTEPYSILLLFSLGVTKGKWGSLAAGLM 605

Query: 601 SFKHHYDANTPLAQVMPELVQDYPDTYANMGIHDLGDKMFAWLRENNPGARLNAAYSTLP 660
            FK HYD N+ L QVMPEL+  + + YA MG+ DL ++M   +  +N    ++AA+S LP
Sbjct: 606 EFKRHYDGNSALEQVMPELLASHAERYAGMGLRDLAEEMHQDMLASNLLQNMDAAFSLLP 665

Query: 661 VAEITPRDAYNAIVNNNIEMVAIENLPGRIAANSVIPYPPGIPMLLSGENFGDENSPQVG 720
               +PR+ Y  +V   IE +A+ ++  R  A  ++PYPPGIP+++ GE  G +    V 
Sbjct: 666 DPVSSPRETYARLVKGEIEQIAVRDMLDRTVAVQIVPYPPGIPLMMPGEKAGADKRAIVD 725

Query: 721 YLRSLQSWDHHFPGFEHETEGTEI 744
           YL +++ +D HFPGF H+  G E+
Sbjct: 726 YLLAMELFDSHFPGFGHDNHGVEV 749


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: 1443
Number of extensions: 64
Number of successful extensions: 4
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