GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruI in Desulfovibrio vulgaris Miyazaki F

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate 8501148 DvMF_1883 acetolactate synthase catalytic subunit (RefSeq)

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__Miya:8501148
          Length = 615

 Score =  239 bits (609), Expect = 3e-67
 Identities = 188/533 (35%), Positives = 250/533 (46%), Gaps = 28/533 (5%)

Query: 26  PQKTLTAGQALV-RLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMA 83
           P+K    G  LV RLL   G+D + GIPG   L LY  L  +G IRHVL RHEQGAGFMA
Sbjct: 21  PRKRQPNGADLVIRLLERQGIDVIAGIPGGANLPLYDALGRAGSIRHVLARHEQGAGFMA 80

Query: 84  DGYARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHET 143
            G ARV+G+P V F  +GPG TN  TAI  A  DSVP++ I+       LG       + 
Sbjct: 81  QGMARVTGRPAVFFATSGPGATNTLTAIADAKLDSVPVVCITG---QVPLGLVGSDAFQE 137

Query: 144 QDQRAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWS 203
            D   M+ P+T  + L  S E+L E+I  A+ +  S RP PV + IP +V  A V     
Sbjct: 138 VDIYGMSIPVTKHNFLVRSVEELAEVIPAAFRIAASGRPGPVLVDIPKNVQMAEVD---Q 194

Query: 204 AAVARRPGRGVPCS------EALRAAAERLAAARRPMLIAGGGALAAG--EALAALSERL 255
           A     P  G P +        +  AA  L AA+RPML  GGG +A+G  +    L+ER 
Sbjct: 195 AVFDNPPQPGQPAAPPAPDPAGISRAAALLNAAQRPMLYLGGGVVASGASDMAVQLAERA 254

Query: 256 AAPLFTSVAGKGLLPPDAPLNAGASLCVAPGWE--MIAEADLVLAVGTEMADTDFWR-ER 312
             P   ++   G +P   PL+ G     A      ++AE D++L  G    D    + ER
Sbjct: 255 GLPTVMTLMALGAMPAGHPLSLGMLGMHAARHTNLLLAECDVLLVAGARFDDRAVGKAER 314

Query: 313 LPLSGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEA---RDSAPAAARVA 369
                 +I +DID  + +   P    + GD    L  LL  L   A   R++        
Sbjct: 315 FCPGATIIHIDIDESELDKILPVHCGITGDVGLALAELLPLLRTRAEAGREAWLTRVEEC 374

Query: 370 RLRAEIRAAHAPLQALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHP 429
           R R       A        ++   A A+  DA V+TD+ Q       A+  R PR WL  
Sbjct: 375 RRRHPFVMPGADDPRTPYGLIRCAADAVDHDAIVATDVGQHQMRTAQAYPLRGPRRWLTS 434

Query: 430 TGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNND 489
            G GT+G+GLPA IGA L  P+   L   GDG      QELATA+EE    + +LL +N+
Sbjct: 435 GGLGTMGFGLPAAIGAALARPEATVLCFTGDGSLQMNIQELATAAEE-GVNVKILLADNN 493

Query: 490 ALGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLR 540
           ALG +R   ++            R  DFA +   +G       DLD  E  LR
Sbjct: 494 ALGLVRQQQELFYEGRLVASTYRRKVDFARIAEGFGVPA---VDLDASEHPLR 543


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: 976
Number of extensions: 61
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 559
Length of database: 615
Length adjustment: 37
Effective length of query: 522
Effective length of database: 578
Effective search space:   301716
Effective search space used:   301716
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