Alignments for a candidate for aruI in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for aruI in Sinorhizobium meliloti 1021

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate SMc04455 SMc04455 thiamine pyrophosphate protein

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__Smeli:SMc04455
          Length = 548

 Score =  172 bits (437), Expect = 2e-47
 Identities = 166/520 (31%), Positives = 240/520 (46%), Gaps = 50/520 (9%)

Query: 31  TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90
           T GQ +V  LA  GV  +  +PG   L +   L  + I  V+ R E GA  MAD + R++
Sbjct: 3   TGGQLVVEALAANGVKRISCVPGESYLAVLDALYDADIEVVVCRQEGGAAMMADAWGRLT 62

Query: 91  GKPGVCFVITGPGVTNVATAIGQAYADSVP-LLVISSVNHSASLGKGWGCLHETQDQRAM 149
           G+PG+C V  GPG TN +  +  A  DSVP +L I  V   A   + +    E + +RA 
Sbjct: 63  GEPGICMVTRGPGATNASAGLHVARQDSVPMILFIGQVQREAREREAF---QEIEYRRAF 119

Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARR 209
           T  +  +      P ++PE + RA+AV  S RP PV +++P D+L    + +  AA A +
Sbjct: 120 T-EVAKWVGEIDDPARIPEFVTRAFAVATSGRPGPVVLTLPEDMLTQ--STEAPAARAYQ 176

Query: 210 PGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALA---ALSERLAAPLFTSVAGK 266
           P    P    +   AE L+ A+RP+ I GG   +A E++A   + +ER   P+  S   +
Sbjct: 177 PVESHPGPSQIAKLAELLSTAKRPIAILGGTRWSA-ESVAGFQSFAERWQLPVGCSFRRQ 235

Query: 267 GLLPPDAPLNAG-ASLCVAPGWE-MIAEADLVLAVG---TEMADTDFWRERLPLSGE-LI 320
            L     P  AG   + + P     I EADLVL VG   +EM  + +    +P   + L+
Sbjct: 236 MLFDHLHPNYAGDVGIGINPSLAGEIREADLVLLVGGRFSEMPSSGYTLIDVPYPRQTLV 295

Query: 321 RVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAE-IRAAH 379
            V  DP +    Y   +A+    R  + AL    P         +AR   + A  ++ + 
Sbjct: 296 HVHPDPGELGRVYRPDLAIAASPRDFVAALSNLTPSA---EPHWSARTGEMHAAYLKWST 352

Query: 380 APLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH----------- 428
            P +      +  I   L A+    T  T  A  GNYA       +WLH           
Sbjct: 353 PPEKGPGDVQMGPIVNWLEANTGPETIFTNGA--GNYA-------TWLHRFHRFRRYGTQ 403

Query: 429 -PTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWN 487
                G++GYGLPA + AK   P R  +   GDG FL   QE ATA    + P++VL+ N
Sbjct: 404 AAPASGSMGYGLPAAVAAKHLHPDREVVCFAGDGCFLMHGQEFATA-VRYELPIIVLVVN 462

Query: 488 NDALGQIRDDMLGLDIEPVGVLP----RNPDFALLGRAYG 523
           N   G IR   +  + E  G +      NPDFA L RAYG
Sbjct: 463 NGIYGTIR---MHQEREYPGRVSATDLTNPDFAALARAYG 499


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: 766
Number of extensions: 47
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: 559
Length of database: 548
Length adjustment: 36
Effective length of query: 523
Effective length of database: 512
Effective search space:   267776
Effective search space used:   267776
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