GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruI in Klebsiella michiganensis M5al

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate BWI76_RS27815 BWI76_RS27815 acetolactate synthase catalytic subunit

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__Koxy:BWI76_RS27815
          Length = 562

 Score =  252 bits (643), Expect = 3e-71
 Identities = 171/473 (36%), Positives = 252/473 (53%), Gaps = 18/473 (3%)

Query: 31  TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGAGFMADGYARV 89
           T  Q +V LL   G+ TV GIPG   L +Y  L  S  IRH+L RHEQGAGF+A G AR 
Sbjct: 14  TGAQLVVHLLERQGITTVSGIPGGSILPIYDALSQSTQIRHILARHEQGAGFIAQGMART 73

Query: 90  SGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAM 149
            GKP VC   +GPG TN+ TAI  A  DS+PL+ I+    ++ +G       +  D   +
Sbjct: 74  EGKPAVCMACSGPGATNLITAIADARLDSIPLVCITGQVPASMIGTD---AFQEVDTYGI 130

Query: 150 TAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARR 209
           + PIT  + L  +  +LP++++ A+ +  S RP PV I IP DV AA +  D       R
Sbjct: 131 SIPITKHNYLVRNIAELPQVMSDAFRIAQSGRPGPVWIDIPKDVQAATIELDALPEPGAR 190

Query: 210 PGRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKGLL 269
                  S ++R AA  + AA+RP+L  GGG + A E +  L+E+   P   ++   G+L
Sbjct: 191 MAAPEFDSASVREAAAMINAAQRPVLYLGGGVINAPEHIRQLAEKANLPTTQTLMALGML 250

Query: 270 PPDAPLNAG-ASLCVAPGWEMI-AEADLVLAVGTEMADTDFWR-ERLPLSGELIRVDIDP 326
           P   PL+ G   +  A     I  EADL++ +G    D    + E+   + ++I VDID 
Sbjct: 251 PKAHPLSLGMLGMHGARSTNFILQEADLLVVLGARFDDRAIGKTEQFCPNAKIIHVDIDR 310

Query: 327 RKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAAARVARLRAE----IRAAHAPL 382
            +      + VA++GD  + LE L+ ++  EA+  +     VA L+ E    I     PL
Sbjct: 311 SELGKIKQAHVAIQGDVGEVLEQLIPQV--EAQPRSAWLQLVADLQREFPCTIPQEQDPL 368

Query: 383 QALHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLHPTGYGTLGYGLPAG 442
              H  +++ +AA +  +A V+TD+ Q       A+    PR WL   G GT+G+GLPA 
Sbjct: 369 S--HYGLINAVAACVDDEAIVTTDVGQHQMWVAQAYPLNRPRQWLTSGGLGTMGFGLPAA 426

Query: 443 IGAKLGAPQRPGLVLVGDGGFLYTAQELATASE-ELDSPLVVLLWNNDALGQI 494
           +GA L  PQR  +   GDG  +   QE+ATA+E +LD  + ++L NN+ALG +
Sbjct: 427 VGAALANPQRKVICFSGDGSLMMNIQEMATAAENQLD--VKIILMNNEALGLV 477


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: 754
Number of extensions: 39
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:

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