GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aruI in Pseudomonas fluorescens FW300-N2C3

Align Probable 2-ketoarginine decarboxylase AruI; 2-oxo-5-guanidinopentanoate decarboxylase; 5-guanidino-2-oxopentanoate decarboxylase; EC 4.1.1.75 (characterized)
to candidate AO356_17755 AO356_17755 hypothetical protein

Query= SwissProt::Q9HUI8
         (559 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_17755 AO356_17755
           hypothetical protein
          Length = 543

 Score =  444 bits (1142), Expect = e-129
 Identities = 260/535 (48%), Positives = 329/535 (61%), Gaps = 15/535 (2%)

Query: 31  TAGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSGIRHVLTRHEQGAGFMADGYARVS 90
           T G+ LV+LL  YGV+ VFGIPGVHT+ELYRGL  S IRHV  RHEQGAGFMADGYARVS
Sbjct: 3   TCGEVLVKLLEGYGVEQVFGIPGVHTVELYRGLARSSIRHVTPRHEQGAGFMADGYARVS 62

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

Query: 151 APITAFSALALSPEQLPELIARAYAVFDSERPRPVHISIPLDVLAAPVAHDWSAAVARRP 210
             + AFS   +S  +LP ++ARA+AVF + RPRPVHI IPLDVL    A    A+V    
Sbjct: 123 GGVAAFSHTLMSAAELPGVLARAFAVFQAGRPRPVHIEIPLDVLVED-ADALLASVPVNI 181

Query: 211 GRGVPCSEALRAAAERLAAARRPMLIAGGGALAAGEALAALSERLAAPLFTSVAGKGLLP 270
            R      A++  A+ LA ARRP+++ GGGA+ A   L  L+ERL AP+  ++  KGLLP
Sbjct: 182 SRAGAAPGAVKQMADLLATARRPLILVGGGAIDARAELTELAERLGAPVALTINAKGLLP 241

Query: 271 PDAPLNAGASLCVAPGWEMIAEADLVLAVGTEMADTDF---WRERLPLSGELIRVDIDPR 327
              PL  G++  +     ++AEAD+VLA+GTE+A+TD+   +     + G L+R+DIDP 
Sbjct: 242 ARHPLLIGSTQSLVVTRALVAEADVVLAIGTELAETDYDITFAGGFEIPGALLRIDIDPD 301

Query: 328 KFNDFYPSAVALRGDARQTLEALLVRL---PQEARDSAPAAARVARLRAEIRAAHAPLQA 384
           +    YP  +AL  DA     ALL  L   P   R +    AR ARLRAE++ +      
Sbjct: 302 QTVRNYPPHLALVADAGVAARALLDELDQRPLAERQADWGPARAARLRAELQGSWDAATR 361

Query: 385 LHQAILDRIAAALPADAFVSTDMTQLAYTGNYAFASRAPRSWLH-PTGYGTLGYGLPAGI 443
                LD +   LP   FV  D TQ  YTGN  F    PR W +  TGYGTLGY LPA I
Sbjct: 362 AQTVFLDTVLQTLPEAVFVG-DSTQPVYTGNLTFNPEQPRRWFNSSTGYGTLGYALPAAI 420

Query: 444 GAKLGAPQ----RPGLV-LVGDGGFLYTAQELATASEELDSPLVVLLWNNDALGQIRDDM 498
           GA LG       RP +V L+GDGG  +T  ELA+A  E  +P++VLLWNN    +I+  M
Sbjct: 421 GAWLGGKDLGHGRPAVVCLIGDGGLQFTLPELASA-VEASTPVIVLLWNNQGYEEIKKYM 479

Query: 499 LGLDIEPVGVLPRNPDFALLGRAYGCAVRQPQDLDELERDLRAGFGQSGVTLIEL 553
           L   IEPVGV    PDF  + +A GC  +   D+  L   L A   + G TLIE+
Sbjct: 480 LNRAIEPVGVDIYTPDFIGVAKALGCFAQAIDDVPSLRAALLAARERQGPTLIEI 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: 842
Number of extensions: 31
Number of successful extensions: 7
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: 543
Length adjustment: 36
Effective length of query: 523
Effective length of database: 507
Effective search space:   265161
Effective search space used:   265161
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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