GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Dinoroseobacter shibae DFL-12

Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate 3607832 Dshi_1240 SMP-30/Gluconolaconase/LRE domain protein (RefSeq)

Query= uniprot:B2UIY8
         (300 letters)



>FitnessBrowser__Dino:3607832
          Length = 286

 Score =  120 bits (302), Expect = 3e-32
 Identities = 97/289 (33%), Positives = 127/289 (43%), Gaps = 26/289 (8%)

Query: 17  CGVGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTN-NWPLPEMAGCIAMAPNGWAM-A 74
           C +GE P+WH   Q L+W DI G+ +   +   G T   W   EM        +   + A
Sbjct: 11  CALGEGPLWHPERQQLFWFDITGQRMLSRD---GDTPLEWQFDEMVSAAGWVDHDTLLIA 67

Query: 75  METGIFLAPPPSPGIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTMVLDTSLGLP 134
            ET +         +  G  + +A +   RP+ R NDGR D  G FW GTM      G  
Sbjct: 68  SETALVTFD-----LAEGESRFVAPLEADRPETRSNDGRADPWGGFWIGTMGKSAEPGA- 121

Query: 135 LGKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHASRQTVWAFDYDIDT 194
            G +YRL       G +  V+ D+ + N L F       Y +D+  +RQ V     D D 
Sbjct: 122 -GAIYRLF-----DGTLRRVVRDVTISNALCFDAAQSCAYYADT-PTRQ-VMRLPLDGDG 173

Query: 195 GTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRLDRSIAIPTSKP 254
                  V +D+ A    PDGA  DA G  WI    AG V    PDG   R++A      
Sbjct: 174 WPSGPATVAVDLRAEGLNPDGAVTDAAGNLWIAQWGAGRVACHAPDGTFLRALACGGRHS 233

Query: 255 AMCAFGGPGLDTLFVTSIRIG---DD----PLSGATFAVRPGVTGLPEP 296
           +  AFGGP LD LF+T+ R G   DD    P +G  FA      GLPEP
Sbjct: 234 SCPAFGGPDLDQLFITTAREGLSADDIAAAPENGCVFAAEGVARGLPEP 282


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: 317
Number of extensions: 23
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: 286
Length adjustment: 26
Effective length of query: 274
Effective length of database: 260
Effective search space:    71240
Effective search space used:    71240
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