GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Phaeobacter inhibens BS107

Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate GFF719 PGA1_c07340 Gluconolactonase

Query= uniprot:B2UIY8
         (300 letters)



>FitnessBrowser__Phaeo:GFF719
          Length = 290

 Score =  118 bits (295), Expect = 2e-31
 Identities = 90/287 (31%), Positives = 136/287 (47%), Gaps = 27/287 (9%)

Query: 16  QCGVGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMAPNGWAMAM 75
           +C +GE P+WH   + L+W DI  + L   +   G+   W   +   C++ A  GW    
Sbjct: 19  RCTLGEGPLWHPTRRQLFWFDILEKRLL--SVAGGKEIIWQFDD---CVSAA--GWVD-- 69

Query: 76  ETGIFLAPPPSP---GIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTMVLDTSLG 132
           ET + +A   +     IE G    L  +   +P  R NDGR D  G FW GTM  +   G
Sbjct: 70  ETTLIMASARALWRFDIESGARTHLIDLEADQPLTRSNDGRADPWGGFWIGTMGYNAEFG 129

Query: 133 LPLGKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHAS---RQTVWAFD 189
           L  G +YR        G +  ++ +  + N + F+P+    Y +D+      RQ + A D
Sbjct: 130 L--GAIYRY-----YQGELRQLVANQTITNAICFAPDKSCAYFTDTKTGKIMRQPLAAED 182

Query: 190 YDIDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRLDRSIAI 249
                G P    VFID++     PDGA VDA+G +W     A  V  +TP G L    ++
Sbjct: 183 -GWPIGAPS---VFIDLSGEDFGPDGAIVDAEGRFWNAQWGASRVAVYTPTGELTEIYSV 238

Query: 250 PTSKPAMCAFGGPGLDTLFVTSIRIG-DDPLSGATFAVRPGVTGLPE 295
           PT++ +  A GG  L  LF+T+   G DDP +G T++++    G  E
Sbjct: 239 PTAQASCPALGGASLSYLFITTAADGLDDPAAGKTYSIQTTAKGQRE 285


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: 292
Number of extensions: 16
Number of successful extensions: 3
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: 290
Length adjustment: 26
Effective length of query: 274
Effective length of database: 264
Effective search space:    72336
Effective search space used:    72336
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