GapMind for catabolism of small carbon sources

 

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

Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate PfGW456L13_2118 L-arabinolactonase (EC 3.1.1.15)

Query= uniprot:B2UIY8
         (300 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2118
          Length = 291

 Score =  142 bits (359), Expect = 7e-39
 Identities = 102/290 (35%), Positives = 138/290 (47%), Gaps = 35/290 (12%)

Query: 19  VGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMAPNGWAM-AMET 77
           +GE P W A  QALYW DI G+   R          W +PE         +G A+ A+ +
Sbjct: 13  LGEGPFWDAPTQALYWVDIAGKQALR--LIGANVQIWQMPEHVSAFIPCESGDALVALSS 70

Query: 78  GIFLAPPPSPGIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTMVLDTSLG---LP 134
           G++     SPG  L P   L  VA  +P  R N+ RCD QGR W GTM  +       LP
Sbjct: 71  GVYRLDLDSPG--LAPRLTLFCVADPQPGNRPNEARCDAQGRLWLGTMQNNIGANGEDLP 128

Query: 135 L----GKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDS-------HASRQ 183
           +    G L+R+D    R GRV  ++ +L +PN L +S +  ++Y  DS       H  R 
Sbjct: 129 IVHRSGGLFRID----RAGRVAPLLRNLGIPNTLLWSDDATSVYFGDSLDGTLYRHFIR- 183

Query: 184 TVWAFDYDIDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRL 243
           T  A D       PH R          G PDG+A+DA+G  W    D   + R + DG++
Sbjct: 184 TDGALDAPQVWFGPHER----------GVPDGSAMDAEGFIWNARWDGNCLLRLSLDGKV 233

Query: 244 DRSIAIPTSKPAMCAFGGPGLDTLFVTSIRIG-DDPLSGATFAVRPGVTG 292
           DR I +P S+P  C FGG  L TL++TS       PL GA  ++   V G
Sbjct: 234 DRIIELPVSRPTSCVFGGSDLKTLYITSAASPLGHPLDGAVLSIAVDVPG 283


Lambda     K      H
   0.322    0.140    0.466 

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: 372
Number of extensions: 28
Number of successful extensions: 4
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: 300
Length of database: 291
Length adjustment: 26
Effective length of query: 274
Effective length of database: 265
Effective search space:    72610
Effective search space used:    72610
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 (21.9 bits)
S2: 48 (23.1 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