GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aruI in Paraburkholderia bryophila 376MFSha3.1

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate H281DRAFT_03007 H281DRAFT_03007 acetolactate synthase-1/2/3 large subunit

Query= SwissProt::Q9HUI8
         (559 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03007 H281DRAFT_03007
           acetolactate synthase-1/2/3 large subunit
          Length = 587

 Score =  175 bits (444), Expect = 4e-48
 Identities = 147/485 (30%), Positives = 219/485 (45%), Gaps = 30/485 (6%)

Query: 30  LTAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARV 89
           ++ G  + + L N GVDT+F + G H +++Y G    GIR +  RHEQ A   ADGYAR 
Sbjct: 31  VSGGHLVAKALKNEGVDTIFTLCGGHIIDIYDGCVDEGIRIIDVRHEQVAAHAADGYARQ 90

Query: 90  SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAM 149
           +GK G      GPG TN  T I  A+    P+L I      A      G L +      M
Sbjct: 91  TGKLGCVVTTAGPGCTNAVTGIATAFRSESPILHIG--GQGALTQHKMGSLQDLPHVDIM 148

Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARR 209
            APIT F+A   S E++ ++I+ A     +  P P ++ IP DVL   V  D S AV  +
Sbjct: 149 -APITKFAASVSSTERVADMISMAARECFNGAPGPAYLEIPRDVLDREV--DLSRAVVPQ 205

Query: 210 PG------RGVPCSEALRAAAERLAAARRPMLIAGGGALAA--GEALAALSERLAAPLFT 261
           PG      + +     +   A+ L  + RP ++ G     A   E   AL   L  P + 
Sbjct: 206 PGHYRASTKSIGDPRDIEKLADILVNSERPAILYGQQVWTARGHEEAIALLRGLDIPGYF 265

Query: 262 SVAGKGLLPPDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDFWRERLPLSGELIR 321
           + A +GLLPP  P +   +   A      A AD+++ VGT       + +R+     L++
Sbjct: 266 NGASRGLLPPGDPHHFDRTRSQA-----FANADVLIVVGTPFDFRMGYGKRISKELTLVQ 320

Query: 322 VDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAAR--VARLR-AEIRAA 378
           +D+D R         + L GD    L A+L       +D    A R  +A+L+ AE  A 
Sbjct: 321 IDMDYRTVGKNRDIDLGLVGDPGAILAAVLQAASGRLKDDKRQARRKWMAQLQDAEATAT 380

Query: 379 H--APLQALHQAILDRIAAALPADAFVSTDMTQLAYTGN------YAFASRAPRSWLHPT 430
               PL   +   +     A   + F++ D   +   G+       A   R P  W+ P 
Sbjct: 381 EKLMPLFKSNSTPIHPYRVAYELNEFLADDTVYIGDGGDVVTISAQAVRPRRPGQWMDPG 440

Query: 431 GYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDA 490
             G+LG G    + AK+  PQ+  L   GDG F  TA ++ TA+    +P + ++ NN A
Sbjct: 441 ALGSLGVGTGFALAAKIAHPQKEVLCYYGDGSFGMTAFDMETAN-RFGAPYLAVIGNNSA 499

Query: 491 LGQIR 495
           + QIR
Sbjct: 500 MNQIR 504


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: 779
Number of extensions: 50
Number of successful extensions: 6
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: 587
Length adjustment: 36
Effective length of query: 523
Effective length of database: 551
Effective search space:   288173
Effective search space used:   288173
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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