GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruI in Shewanella amazonensis SB2B

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 6939187 Sama_3281 acetolactate synthase 2 catalytic subunit (RefSeq)

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__SB2B:6939187
          Length = 556

 Score =  221 bits (563), Expect = 6e-62
 Identities = 173/541 (31%), Positives = 254/541 (46%), Gaps = 32/541 (5%)

Query: 28  KTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYA 87
           +T+    A++++LA +GV+TVFG PG   + +Y  L GS + H L RHEQGAGF A GYA
Sbjct: 4   QTMRGADAVIKVLAAHGVNTVFGYPGGAIMPIYDALYGSEVEHTLCRHEQGAGFAAVGYA 63

Query: 88  RVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQR 147
           R SGK GVCF  +GPG TN+ TA+  A  DSVP++ I+    ++ +G       +  D  
Sbjct: 64  RASGKTGVCFATSGPGATNLITALADALLDSVPVVAITGQVSTSVIGTD---AFQEIDVL 120

Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWS-AAV 206
            M+   T  S +  + ++L   + RA+ +  S RP PV + IP D+  A + +     AV
Sbjct: 121 GMSLSCTKHSFMVQTVDELVPTLYRAFELAASGRPGPVLVDIPKDIQIAKLEYRAPLLAV 180

Query: 207 ARRPGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERLAAPLFTSVA 264
           A  P       +A RA    +AAA++PML  GGG   AG  E L    +    P   ++ 
Sbjct: 181 ADEPKVQDADIDAARAL---IAAAKKPMLYVGGGVGMAGAVEPLRHFIKATYMPSVATLK 237

Query: 265 GKGLLPPDAP-------LNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWR-ERLPLS 316
           G G +P   P       ++ G +  +A     + E DL++ VG    D    R      +
Sbjct: 238 GLGAIPHGTPGYLGMLGMHGGKAANLA-----VQECDLLMVVGARFDDRVTGRLASFAPN 292

Query: 317 GELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAEIR 376
            +++ +DID  +        VA+  + R  L  L ++L     D  P  A V  L AE R
Sbjct: 293 AKVLHLDIDAAELGKLRQPDVAIAAELRVVLPMLEMQL-----DIDPWRAEVEALAAEHR 347

Query: 377 --AAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGT 434
               H        A+L R+A  LP D+ VS D+ Q           R P   L   G GT
Sbjct: 348 WDYNHPGSLIYAPAMLRRLANKLPEDSVVSCDVGQHQMWVAQHMHFRRPEDHLSSAGLGT 407

Query: 435 LGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQI 494
           +G+GLPA IGA++  P    + + GDG F+   QEL T       P+ +LL +N  LG +
Sbjct: 408 MGFGLPAAIGAQMARPDATVVAVSGDGSFMMNVQELTTIKRR-KLPVKILLIDNQRLGMV 466

Query: 495 R--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIE 552
           +    +   +      L  NPDF  L  A+    R     +E+E  L       G  L+ 
Sbjct: 467 KQWQQLFFEERYSETNLSDNPDFVALASAFDIPGRTIFAAEEVEEALTEMLTSKGPYLLH 526

Query: 553 L 553
           +
Sbjct: 527 V 527


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: 727
Number of extensions: 37
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: 556
Length adjustment: 36
Effective length of query: 523
Effective length of database: 520
Effective search space:   271960
Effective search space used:   271960
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