Alignments for a candidate for aruI in Desulfovibrio vulgaris Miyazaki F

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 8499376 DvMF_0153 acetolactate synthase, large subunit, biosynthetic type (RefSeq)

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__Miya:8499376
          Length = 562

 Score =  241 bits (614), Expect = 7e-68
 Identities = 176/541 (32%), Positives = 254/541 (46%), Gaps = 20/541 (3%)

Query: 30  LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARV 89
           L   + L+  L   GVD +FG PG   +++Y  LP   IRH+L RHEQ A   ADG+AR 
Sbjct: 3   LNGARILLECLKREGVDVLFGYPGGAVIDIYDELPRHDIRHILVRHEQAAVHAADGFARA 62

Query: 90  SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAM 149
           SGK GVC V +GPG TN  T I  AYADS+P++V++    +  +G       +  D   +
Sbjct: 63  SGKVGVCLVTSGPGATNTVTGIATAYADSIPMVVLTGQVPTPLIGND---AFQEVDIVGI 119

Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARR 209
           T P T  + L      L  ++ +A+ +  S RP PV + +P DV+ A     W   V  R
Sbjct: 120 TRPCTKHNYLVKDVRDLARVLRQAFYLARSGRPGPVLVDLPKDVMQAKTEFVWPEDVKLR 179

Query: 210 PGRGV--PCSEALRAAAERLAAARRPMLIAGGGALA--AGEALAALSERLAAPLFTSVAG 265
                  P    LR A E L  A+RP+  AGGG +   A E L  L+  L+ P+ +++ G
Sbjct: 180 SYNPTYRPNLNQLRRAVEALIEAKRPLFFAGGGVIMSDASEELGWLARTLSIPVTSTLMG 239

Query: 266 KGLLPPDAPLNAG--ASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSG-ELIRV 322
            G  P D PL  G         G + +  AD ++AVG    D    R     SG  +I +
Sbjct: 240 LGAFPGDDPLWLGMIGMHGTYAGNKAVNNADCIVAVGARFDDRVTGRLSAFASGARIIHI 299

Query: 323 DIDPRKFNDFYPSAVALRGDARQTL----EALLVRLPQE--ARDSAPAAARVARLRAEIR 376
           DIDP          + + GD R+ L    E    RL ++  A    P   +V+  R E  
Sbjct: 300 DIDPTSIRKNVQVDIPVVGDCRKALAGIREIATTRLAEKDWATAHEPWLTQVSAWRTEQP 359

Query: 377 AAHAPLQALH-QAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTL 435
             +    ++  Q +++ I +    DA V+T++ Q        F  R PR+ L   G GT+
Sbjct: 360 LTYVKNGSIKPQQVVETIFSITRGDAIVTTEVGQNQMWTAQFFTFRKPRTLLTSGGLGTM 419

Query: 436 GYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIR 495
           GYG PA IGA+   P +  + + GDG      QELATA      P+ +++ NN  LG +R
Sbjct: 420 GYGFPAAIGAQFAFPDKLVIDMAGDGSIQMNIQELATAVCN-KLPIKIVILNNGYLGMVR 478

Query: 496 --DDMLGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553
              ++          +   PDF  L  AYG    +  +  ELE  LRA F      +I++
Sbjct: 479 QWQELFYQRNYCSTCMEAQPDFVKLAEAYGAEGYRITEAGELESTLRAAFASPHTAVIDV 538

Query: 554 R 554
           R
Sbjct: 539 R 539


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: 761
Number of extensions: 42
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: 562
Length adjustment: 36
Effective length of query: 523
Effective length of database: 526
Effective search space:   275098
Effective search space used:   275098
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:

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