GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruI in Phaeobacter inhibens BS107

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate GFF1906 PGA1_c19360 acetolactate synthase isozyme, large subunit

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__Phaeo:GFF1906
          Length = 601

 Score =  199 bits (505), Expect = 3e-55
 Identities = 171/566 (30%), Positives = 260/566 (45%), Gaps = 51/566 (9%)

Query: 31  TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90
           T  + +V  L    V+ VFG+ G   + +   L  S I  +  RHEQ A   AD YARV+
Sbjct: 14  TVAEHIVDFLGRRNVEHVFGLCGHTNIAVLAALADSPIDFITVRHEQIASHAADAYARVT 73

Query: 91  GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGK---GWGCLHETQDQR 147
           G+  V      PG+TN AT +  A  D VP++VI+    +   GK       LH    Q 
Sbjct: 74  GRASVVLSHLSPGLTNCATGVANAALDCVPMVVIAGDIPTHYYGKHPHQEVNLHADAAQW 133

Query: 148 AMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVA 207
            +  P    +      + + E++ +A+ + +S +P PV +++P+D+ +  ++ D    +A
Sbjct: 134 EIYRPFVKRAWRVDRADLMAEILEKAFHLAESGQPGPVLVNVPMDIFSEVISSDTFDRIA 193

Query: 208 RRPGRGVPCS---EALRAAAERLAAARRPMLIAGGGALAAGEALAALSE---RLAAPLFT 261
                 V  S   E  R     LAAA+ P+   GGG L A +A A + E    +  P+  
Sbjct: 194 SNTKTLVKPSMDDETARRIVSGLAAAKDPVAYIGGGILLA-QASAEIEEFATHMGLPIAH 252

Query: 262 SVAGKGLLPPDAPLNAGASLCVAPGWEMIAE----ADLVLAVGTEM--ADTDFWRERLPL 315
           S+ GKG +  D PL  G  +    G E++ +    AD+V AVGT    AD   W      
Sbjct: 253 SLMGKGAVRDDHPLVMG--MTGFWGTELVNQTCLNADVVFAVGTRFKEADCSSWYPGYTF 310

Query: 316 S-------GELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAP----- 363
           +        ++I +DI+P++    YP+ + +  DA+  L      L + A+D  P     
Sbjct: 311 NIGAKGNDTKVIHIDIEPQEIGRNYPTEIGVVADAKAALRV----LTRVAKDMYPDGFNR 366

Query: 364 --AAARVARLRAEIRAAHAPLQA------LHQAILDRIAAALPADAFVSTDMTQLAYTGN 415
               A +A  R + +A++  +Q       + + IL     ALP DA ++TD+        
Sbjct: 367 TEKKAEIAAFREDFKASNVEMQTSAAFPMMPERILADTRIALPDDAIITTDVGWNKNGVG 426

Query: 416 YAFASRAPRSWLHPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASE 475
             F    P S L P G+ T+G+G PA IGAKL AP+R  L LVGDGGF      LATA  
Sbjct: 427 QQFDILTPGSILTPGGFATMGFGPPAAIGAKLAAPERVVLSLVGDGGFGQNPSMLATA-V 485

Query: 476 ELDSPLVVLLWNNDALGQIRDDM-------LGLDIEPVGVLPRN-PDFALLGRAYGCAVR 527
           EL+  ++ L+ NN+A G I            G         P N P +A + RAYG    
Sbjct: 486 ELNLGIIWLVMNNNAFGTIAGLQKAHYGLTYGTTFPGSAAAPTNGPGYAEIARAYGAEGI 545

Query: 528 QPQDLDELERDLRAGFGQSGVTLIEL 553
           +    DEL   L+A       T++++
Sbjct: 546 RISSADELLPALQAAIASGKPTVLDV 571


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: 820
Number of extensions: 38
Number of successful extensions: 8
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: 601
Length adjustment: 36
Effective length of query: 523
Effective length of database: 565
Effective search space:   295495
Effective search space used:   295495
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