GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruI in Acidovorax sp. GW101-3H11

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate Ac3H11_1601 Acetolactate synthase large subunit (EC 2.2.1.6)

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1601
          Length = 561

 Score =  166 bits (421), Expect = 2e-45
 Identities = 153/520 (29%), Positives = 232/520 (44%), Gaps = 49/520 (9%)

Query: 31  TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90
           T GQ LV+ L  +GV  +F +PG   L +   L  + I   + R E GA  MA+   +++
Sbjct: 10  TGGQILVQQLITHGVKQLFCVPGESYLAVLDALHDADIGVTVCRQEGGAAMMAEAQGKLT 69

Query: 91  GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150
           G+PG+CFV  GPG TN +  +  A+ DS P+++        ++G+      +  D  A+ 
Sbjct: 70  GQPGICFVTRGPGATNASAGVHIAHQDSTPMILFVGQVARGAMGRE---AFQELDYSAVF 126

Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVL--AAPVAHDWSAAVAR 208
             +  +      P ++PELI+RA+ V  S RP PV +++P D+L  AA VA     A+  
Sbjct: 127 GTMAKWVVQIDDPARVPELISRAFHVATSGRPGPVVVALPEDMLTEAATVAD----ALPY 182

Query: 209 RPGRGVPCSEALRAAAERLAAARRPMLIAGGGALA--AGEALAALSERLAAPLFTSVAGK 266
           +     P +  L   A+RL AA+ P+ I GG   +  A     A +E  + P++ S   +
Sbjct: 183 QVTETHPGAAQLAELAQRLQAAKNPVAILGGSRWSEEAVREFTAFAEAWSIPVYCSFRRQ 242

Query: 267 GLLPPDAPLNAG-ASLCVAPG-WEMIAEADLVLAVG---TEMADTDFWRERLPLSGE-LI 320
            L P       G   L V P     I  +DLVL VG   +E+    +    +P   +  +
Sbjct: 243 MLFPATHACYGGDLGLGVNPKLLARIKASDLVLVVGGRLSEVPSQGYELFDIPTPAQSFV 302

Query: 321 RVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIRAAHA 380
            V  D  +    Y    A+    +    AL        R +A  A      +A   AAHA
Sbjct: 303 HVHADADELGKLYRPTQAIHATPQAFTAAL-----NAVRPTASVA-----WKAHTEAAHA 352

Query: 381 PLQALHQ-------------AILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWL 427
              A                 ++  + + LPAD          A   +  +      S L
Sbjct: 353 EYLAWSDPAPIRIPGNLQMGEVMQHLKSVLPADTIFCNGAGNFATWVHRFWPFTTYASQL 412

Query: 428 HPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWN 487
            PT  G++GYGLPAG+G K   PQR  +V  GDG FL   QE ATA  +   P++V+L +
Sbjct: 413 APTS-GSMGYGLPAGVGGKRLWPQREVVVFAGDGDFLMHGQEFATA-VQYGLPILVVLLD 470

Query: 488 NDALGQIRDDMLGLDIEPVGVLP----RNPDFALLGRAYG 523
           N   G IR   +  + E  G +     +NPDF    +A+G
Sbjct: 471 NAMYGTIR---MHQEREYPGRISATQLKNPDFKAYAQAFG 507


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: 738
Number of extensions: 47
Number of successful extensions: 3
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: 561
Length adjustment: 36
Effective length of query: 523
Effective length of database: 525
Effective search space:   274575
Effective search space used:   274575
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.

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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:

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:

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:

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:

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