Alignments for a candidate for aruI in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for aruI in Marinobacter adhaerens HP15

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate GFF1038 HP15_1017 acetolactate synthase, large subunit, biosynthetic type

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__Marino:GFF1038
          Length = 566

 Score =  204 bits (519), Expect = 7e-57
 Identities = 163/537 (30%), Positives = 243/537 (45%), Gaps = 21/537 (3%)

Query: 30  LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGS-GIRHVLTRHEQGAGFMADGYAR 88
           +   Q ++     + + TVFG PG   + LY  L    G+ HVL RHEQG    ADGYAR
Sbjct: 1   MNGAQHILEAFHRHNISTVFGYPGGCIMPLYDALVDDVGVEHVLCRHEQGCALAADGYAR 60

Query: 89  VSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRA 148
            SGK GVC   +GPG TN+ T +  A+ DS+P+LVI+    S  +G       ET D   
Sbjct: 61  ASGKLGVCIATSGPGATNLITGVANAHRDSIPMLVITGQVPSGLIGT--DAFQET-DVLG 117

Query: 149 MTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVAR 208
           MT  I   S L    + LP ++  A  +  S RP PV I IP D+L + VA     A   
Sbjct: 118 MTLGIVKHSYLINDADSLPIIMEEAIELAQSGRPGPVWIDIPKDLLLSDVAD----APFP 173

Query: 209 RPGRGVPCSEALRAAAERLAAARRPMLIAGGGALA--AGEALAALSERLAAPLFTSVAGK 266
           +     P S  L+ A   L AAR+P+L +GGG     A E   A +E  A P   ++ G 
Sbjct: 174 QAQPYEPASPDLKEALAMLRAARKPLLYSGGGISLGHAEENFRAFAESSALPAVVTLKGI 233

Query: 267 GLLPPDAPLNAG--ASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-ERLPLSGELIRVD 323
           G      P N G           + + E DL+L +G  + D    + +    +  +I +D
Sbjct: 234 GNPGKHNPYNLGMLGMHGSRAANKAVDECDLLLVIGARLDDRATGKLDGFAPNARMIHID 293

Query: 324 IDPRKFNDFYPSAVALRGDARQTLEALLVRLPQE--ARDSAPAAARVARLRAEIRAA--H 379
            D  + N    + +A+RGD    L++L   L  +  A        R         AA   
Sbjct: 294 ADAAEINKLRDADLAIRGDLNHILKSLAGELHADPLAISEWQKQCRSWYTTGGFHAADNE 353

Query: 380 APLQAL-HQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYG 438
            PL  +   A + +++   P D  ++ D+ Q        +    PR  L   G GT+G+G
Sbjct: 354 EPLAPITGPAFIRQLSRIAPDDTVIACDVGQHQMWVAQHYDFDHPRHHLTSGGLGTMGFG 413

Query: 439 LPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIR--D 496
           LPA IGA+        + + GDG F+  AQELAT     + P+ +++ +N  LG +R   
Sbjct: 414 LPAAIGAQFADRNSTVINVTGDGSFMMNAQELATI-RRYNLPVKLIVMDNQCLGMVRQQQ 472

Query: 497 DMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553
           ++   + E    L  NPDF  + RA+       +  D++ R +      +G  L+ +
Sbjct: 473 ELFYNNRESQINLDDNPDFVAMARAFDIPALYIERTDQIRRGIETILAYNGPMLLHV 529


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: 741
Number of extensions: 38
Number of successful extensions: 7
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: 566
Length adjustment: 36
Effective length of query: 523
Effective length of database: 530
Effective search space:   277190
Effective search space used:   277190
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: 53 (25.0 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