GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruI in Caulobacter crescentus NA1000

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate CCNA_02185 CCNA_02185 acetolactate synthase large subunit

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__Caulo:CCNA_02185
          Length = 601

 Score =  193 bits (490), Expect = 2e-53
 Identities = 161/531 (30%), Positives = 244/531 (45%), Gaps = 30/531 (5%)

Query: 28  KTLTAGQALVRLLANYGVDTVFGIPGVHTLELYRGL-PGSGIRHVLTRHEQGAGFMADGY 86
           + +T  + +VR L + GV+ +FG PG   L +Y  L     ++H+L RHEQGA   A+GY
Sbjct: 18  RAMTGAEIVVRGLVDQGVEVLFGYPGGAVLPIYDALFHEPRLQHILVRHEQGAAHAAEGY 77

Query: 87  ARVSGKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQ 146
           AR SGKPGV  V +GPG TN  T I  A  DS+P++VI+    +  +G       +  D 
Sbjct: 78  ARSSGKPGVVLVTSGPGATNAITGIMDALMDSIPMVVITGQVPTHLIGTD---AFQEADT 134

Query: 147 RAMTAPITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAV 206
             MT   T  + L      LP++I  A+ +  + RP PV I IP DV  A   +     V
Sbjct: 135 VGMTRSCTKHNYLVKDVRDLPQIIHEAFKIATTGRPGPVLIDIPKDVQFAKGEYFGPGEV 194

Query: 207 ARRPG---RGVPCSEALRAAAERLAAARRPMLIAGGGALAAG-EALAALSERLA---APL 259
           A       R    +  +  AA  +A ARRP+   GGG + AG +A AAL E  A   AP+
Sbjct: 195 ASTHAYAPRTKGDAGRIAEAARMIAQARRPIFYTGGGVINAGPKASAALREFAALTGAPV 254

Query: 260 FTSVAGKGLLPPDAPLNAGASLCVAPGWE---MIAEADLVLAVGTEMADTDFWR-ERLPL 315
            +++ G G  P   P   G  L +   +E    + + D+++ VG    D    R +    
Sbjct: 255 TSTLMGLGAFPAADPAWLG-MLGMHGTFEANNAMHDCDVMICVGARFDDRVTGRLDAFSP 313

Query: 316 SGELIRVDIDPRKFNDFYPSAVALRGDARQTLEALLVRLPQEARDSAPAA-----ARVAR 370
             + I +DIDP   N      + + GDA   LE L+            AA     A++ +
Sbjct: 314 GSKKIHIDIDPSSINKNVRVDLPIVGDAGSVLEDLIAAWKAANLQPNKAALTDWWAQIDQ 373

Query: 371 LRAEIRAAHAPLQAL--HQAILDRI-AAALPADAFVSTDMTQLAYTGNYAFASRAPRSWL 427
            RA    ++    ++   Q  ++R+       D +++T++ Q        F    P  W+
Sbjct: 374 WRARQCLSYRRSDSVIKPQYAIERLYELTKDKDVYITTEVGQHQMWAAQFFRFEEPNRWM 433

Query: 428 HPTGYGTLGYGLPAGIGAKLGAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWN 487
              G GT+GYGLPA +G +L  P    + + G+       QEL+TA  + D P+ + + N
Sbjct: 434 TSGGLGTMGYGLPAALGVQLAHPNSLVVDIAGEASIQMCIQELSTAI-QFDLPVKIFILN 492

Query: 488 NDALGQIR--DDMLGLDIEPVGVLPRNPDFALLGRAYGCA---VRQPQDLD 533
           N+ +G +R    +L  +          PDF  L  AYG        P +LD
Sbjct: 493 NEWMGMVRQWQQLLHGERYSHSYSDSLPDFVKLAEAYGAVGIRCDNPAELD 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: 822
Number of extensions: 42
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: 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