GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Dinoroseobacter shibae DFL-12

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate 3608829 Dshi_2221 ABC transporter related (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_2050
         (263 letters)



>FitnessBrowser__Dino:3608829
          Length = 259

 Score =  250 bits (638), Expect = 2e-71
 Identities = 133/252 (52%), Positives = 173/252 (68%)

Query: 10  TQPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQ 69
           T P+++IR L K YG LEVLKGV +  +RG+VV+LIGSSGSGK+TLLRC N+LE+ Q G 
Sbjct: 5   TVPVIEIRDLHKAYGALEVLKGVSIRAERGDVVSLIGSSGSGKSTLLRCCNLLEDSQRGD 64

Query: 70  IMLDGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKK 129
           ++  GE + +      R    +K + R R    M FQQFNL+ H+T L+NV    + V  
Sbjct: 65  VLFCGEPVTWTGSGLDRRPADKKQVIRIRTNLSMVFQQFNLWAHMTILENVMEAPVTVLG 124

Query: 130 LPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSAL 189
            P  E  A A   L++VG+ ++ D +P QLSGGQQQR AIAR +AM P  +LFDE TSAL
Sbjct: 125 EPPKEVEARARALLDKVGIGDKCDAYPAQLSGGQQQRAAIARGLAMEPKALLFDEPTSAL 184

Query: 190 DPELVGEVLNVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERP 249
           DPEL  EV+ VIK LA +G TML+VTH+MR A +VSD +VF++QG IEE+GPP  LF +P
Sbjct: 185 DPELEQEVVKVIKDLAAEGRTMLIVTHDMRLAADVSDHVVFLHQGLIEEEGPPDILFGQP 244

Query: 250 QSPRLAEFLKNT 261
           +S RL +FL  T
Sbjct: 245 KSARLKQFLSAT 256


Lambda     K      H
   0.320    0.138    0.392 

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: 197
Number of extensions: 6
Number of successful extensions: 1
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: 263
Length of database: 259
Length adjustment: 25
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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: 47 (22.7 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