GapMind for catabolism of small carbon sources

 

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

Align RnsA, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate 3609458 Dshi_2842 basic membrane lipoprotein (RefSeq)

Query= TCDB::Q8DU36
         (349 letters)



>FitnessBrowser__Dino:3609458
          Length = 329

 Score =  129 bits (325), Expect = 8e-35
 Identities = 96/317 (30%), Positives = 157/317 (49%), Gaps = 34/317 (10%)

Query: 39  AIVTDTGGVDDKSFNQSAWEGLQAWGKDNGLSKGNGFDYFQSASESDYATNLDTASSSGY 98
           A++ D GG  DKSFN++A+ G Q W ++ G      +   +  SE+     L   + +G 
Sbjct: 26  ALIFDLGGKFDKSFNEAAFNGAQRWVQETG----GTYREIELTSEAQREQALRRFAEAGN 81

Query: 99  KLIFGIGYALHDAIEKTAADNKNIHYVIIDDVIQKKNNVASVTFADNEAAYLAGIAAAKT 158
             I   G+A  + + + A D  +  + IID V+ + N V SV F ++E +YL G+ AA  
Sbjct: 82  NPIVMTGFAFGNVLGEVAPDYPDTSFAIIDMVVDQPN-VRSVVFNEHEGSYLVGMMAAMA 140

Query: 159 TKSKKVGFVGGVKSEVITRFEKGFEAGVKSVDSSIQIQVDYAG----SFGDAAKGKTIAA 214
           +++  VGF+GG+   +I +F  G+  GVK+ +    +  +  G    ++ D  KG  +  
Sbjct: 141 SETGTVGFIGGMDIPLIRKFACGYAQGVKAANPDATVIQNMTGTTPAAWNDPVKGGELTR 200

Query: 215 AQYASGADVIYQAAGGTGAGVFSEAKAVNEKKKENKKVWVIGVDRDQAAEGKYTSKDGKK 274
           AQ + GADV+Y AAGGTG GV   A         ++ +  IGVD +Q         +   
Sbjct: 201 AQISQGADVVYAAAGGTGVGVLQTA--------ADEDILSIGVDSNQ---------NYLH 243

Query: 275 SNFVLASSLKEVGKAVQLISTNTSKKKFPGGKVTTYGLKDKGV-----DLVPTHLSKEGK 329
              VL S +K V  AV   +  +    F  G +   GL + GV     +     ++ E +
Sbjct: 244 PGEVLTSMMKRVDNAV--FAAMSDGPGFETG-IRVLGLAEDGVGYALDEFNAELVTDEMQ 300

Query: 330 KAVDDAKKKIVSGDVKV 346
            AV++AK KI++G++ V
Sbjct: 301 AAVEEAKAKIIAGEITV 317


Lambda     K      H
   0.310    0.128    0.352 

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: 257
Number of extensions: 16
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: 349
Length of database: 329
Length adjustment: 28
Effective length of query: 321
Effective length of database: 301
Effective search space:    96621
Effective search space used:    96621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 49 (23.5 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