Alignments for a candidate for aruI in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for aruI in Pseudomonas fluorescens GW456-L13

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate PfGW456L13_1794 Acetolactate synthase, large subunit (EC 2.2.1.6)

Query= SwissProt::Q9HUI8
         (559 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1794
          Length = 545

 Score =  436 bits (1121), Expect = e-126
 Identities = 252/535 (47%), Positives = 329/535 (61%), Gaps = 15/535 (2%)

Query: 31  TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90
           T G+ LV+LL NYGV+ VFGIPGVHT+ELYRGL  S I HV  RHEQGAGFMADGYAR S
Sbjct: 3   TCGEVLVKLLENYGVEQVFGIPGVHTVELYRGLARSSINHVTPRHEQGAGFMADGYARTS 62

Query: 91  GKPGVCFVITGPGVTNVATAIGQAYADSVPLLVISSVNHSASLGKGWGCLHETQDQRAMT 150
           GKPGVCF+ITGPG+TN+ TA+GQAYADS+P+LVISSV   + LG G G LHE  +Q A+ 
Sbjct: 63  GKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRSQLGGGRGKLHELPNQGALC 122

Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARRP 210
           A + AFS   +S  +LP ++ARA+A+F + RPRPVHI IPLDVL    A D  A++    
Sbjct: 123 AGVAAFSHTLMSASELPGVLARAFALFQAGRPRPVHIEIPLDVLVEE-ADDLLASLPVNI 181

Query: 211 GRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKGLLP 270
            R      A+   AE LA A+RP+++AGGGA+ A   L  L+E L AP+  ++  KG+L 
Sbjct: 182 DRAGASPSAVSRMAELLAGAKRPLILAGGGAIDAAVELTELAELLDAPVALTINAKGMLA 241

Query: 271 PDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDF---WRERLPLSGELIRVDIDPR 327
              PL  G++  +     ++AEAD+VLA+GTE+A+TD+   +     + G+L+RVDIDP 
Sbjct: 242 SGHPLLIGSTQSLVATRALVAEADVVLAIGTELAETDYDVTFAGGFEIPGKLLRVDIDPD 301

Query: 328 KFNDFYPSAVALRGDARQTLEALLVRLPQEA---RDSAPAAARVARLRAEIRAAHAPLQA 384
           +    YP  VAL  D+R   +ALL  L  ++   R +     R ARLR ++ A       
Sbjct: 302 QTVRNYPPHVALVADSRNAAQALLSALSHKSLAERRNDWGQVRAARLREDLAATWDAPTL 361

Query: 385 LHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH-PTGYGTLGYGLPAGI 443
                L+ +   LP   FV  D TQ  YTGN  F    PR W +  TGYGTLGY LPA I
Sbjct: 362 AQTRFLETVLQELPDAVFVG-DSTQPVYTGNLTFNPERPRRWFNSSTGYGTLGYALPAAI 420

Query: 444 GAKL-----GAPQRPGLVLVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDM 498
           GA L     G  + P + L+GDGG  +T  ELA+A  E  +P++VLLWNN    +I+  M
Sbjct: 421 GAWLGGRIEGGARPPVVCLIGDGGLQFTLPELASA-VEARTPVIVLLWNNQGYEEIKKYM 479

Query: 499 LGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553
           +   IEPVGV    PDF  + +A GCA      +++L   LR    + G TLIE+
Sbjct: 480 VNRAIEPVGVDIYTPDFIGVAKALGCAAEAVSSVEQLRGALRVATDRQGPTLIEI 534


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: 785
Number of extensions: 33
Number of successful extensions: 8
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: 545
Length adjustment: 36
Effective length of query: 523
Effective length of database: 509
Effective search space:   266207
Effective search space used:   266207
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