Alignments for a candidate for aruI in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for aruI in Pseudomonas simiae WCS417

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate GFF2097 PS417_10695 decarboxylase

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__WCS417:GFF2097
          Length = 535

 Score =  858 bits (2216), Expect = 0.0
 Identities = 423/531 (79%), Positives = 471/531 (88%)

Query: 28  KTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYA 87
           K +T GQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYA
Sbjct: 4   KAMTGGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYA 63

Query: 88  RVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147
           RVSGKPGVCFVITGPGVTN ATAIGQAYADS+P+LVISSVN + SLGKGWG LHETQDQR
Sbjct: 64  RVSGKPGVCFVITGPGVTNAATAIGQAYADSIPMLVISSVNSTVSLGKGWGILHETQDQR 123

Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207
           A+TAPITAFSA+ALS E LPEL+ARAYA+FDSERPRPVHIS+PLDVLAAP+  DWS  V 
Sbjct: 124 AITAPITAFSAVALSAEDLPELVARAYAIFDSERPRPVHISVPLDVLAAPIQRDWSNEVV 183

Query: 208 RRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKG 267
           RRP RG+P ++AL   A +LAAA+RPM+IAGGGALAAGEAL  LS +LAAP FTSVAGKG
Sbjct: 184 RRPDRGLPPAKALDQGAAKLAAAKRPMIIAGGGALAAGEALQRLSTQLAAPFFTSVAGKG 243

Query: 268 LLPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGELIRVDIDPR 327
           LLP + PLNAG++LCV PGW++I+EAD+VLAVGTEMADTD+W ERLPL GEL+RVDID R
Sbjct: 244 LLPVNDPLNAGSTLCVEPGWQLISEADVVLAVGTEMADTDYWCERLPLGGELLRVDIDAR 303

Query: 328 KFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHAPLQALHQ 387
           KFNDFYP AVAL+GDA+QT+ ALL RLP  AR++  A + VA L   I + H PLQ++HQ
Sbjct: 304 KFNDFYPCAVALKGDAQQTVLALLERLPTTARNAEAAISTVAALLHAIESGHGPLQSIHQ 363

Query: 388 AILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAGIGAKL 447
           AILDRI A LPA+AF+S+DMTQLAYTGNYA+ SRAPRSWLHPTGYGTLGYGLPAGIGAK 
Sbjct: 364 AILDRIEAELPANAFISSDMTQLAYTGNYAYRSRAPRSWLHPTGYGTLGYGLPAGIGAKF 423

Query: 448 GAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDMLGLDIEPVG 507
           GAPQRPGLVLVGDGGFLYTAQELATA EELDSPLVVLLWNNDALGQIRDDML LDI P+G
Sbjct: 424 GAPQRPGLVLVGDGGFLYTAQELATAVEELDSPLVVLLWNNDALGQIRDDMLSLDIAPIG 483

Query: 508 VLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIELRHACA 558
           VLPRNPDFAL  +A+GC V QP++LDEL+ DLR  F ++GVTLIEL+HACA
Sbjct: 484 VLPRNPDFALFAQAFGCTVNQPRNLDELQTDLRNAFKRNGVTLIELKHACA 534


Lambda     K      H
   0.321    0.136    0.412 

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: 1004
Number of extensions: 36
Number of successful extensions: 1
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: 559
Length of database: 535
Length adjustment: 36
Effective length of query: 523
Effective length of database: 499
Effective search space:   260977
Effective search space used:   260977
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: 52 (24.6 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)
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