GapMind for catabolism of small carbon sources

 

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

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 3610414 Dshi_3795 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q97VF5
         (362 letters)



>FitnessBrowser__Dino:3610414
          Length = 331

 Score =  182 bits (463), Expect = 8e-51
 Identities = 116/323 (35%), Positives = 182/323 (56%), Gaps = 22/323 (6%)

Query: 45  ILEVHNLNVIYDEG----NSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAI 100
           +L  HNL   +  G    N R+++AV+DV+F V  GE LG++GESG GK+T    +++ +
Sbjct: 10  VLSAHNLVKHFPLGGWGKNRRVVRAVDDVTFEVAPGETLGVVGESGCGKSTTARLLVQLL 69

Query: 101 RPPGKIISGKVIFNG-MDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEA 159
                  SG+V F G +    M + EFR+     +  V Q S  +LNP + + +      
Sbjct: 70  GAD----SGEVRFQGHVAGTEMPLKEFRR----HVQMVFQDSYASLNPRMSMLDAIAFGP 121

Query: 160 ISHG--EADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLI 217
             HG  EA+ +R+   A +LL  VGLDP+R    YP +LSGG +QRV IA +L   P++I
Sbjct: 122 TVHGVSEAEAQRI---ARDLLDRVGLDPSRFGPRYPHELSGGQRQRVNIARALAFQPEVI 178

Query: 218 LMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE 277
           ++DE  SALD   +  +L L+ ++ +E  +T V+++HD+  +  +++R++VMY G V E 
Sbjct: 179 VLDEAVSALDKSVEAQVLNLLMDLKRERNLTYVFISHDLNVVRHVSDRVMVMYLGEVAEI 238

Query: 278 GKTEEIIKSPLNPYTSLLVSSIPSLKGEVKVINVPL--DEP-LVSKEKGCPFLARCSKAF 334
           G T E+   P +PYT  L++++PSL  + +    PL  D P  +    GC F  RC++AF
Sbjct: 239 GPTAEMYADPRHPYTRALLAAMPSLDPDRRTTEAPLSGDPPNPIDPPSGCRFHTRCAEAF 298

Query: 335 GRCKEELP-EIRLVYDRKVRCHL 356
           G C  + P  +R+       CHL
Sbjct: 299 GACSAQRPSNLRVGAGHYASCHL 321


Lambda     K      H
   0.319    0.138    0.391 

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: 261
Number of extensions: 14
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: 362
Length of database: 331
Length adjustment: 29
Effective length of query: 333
Effective length of database: 302
Effective search space:   100566
Effective search space used:   100566
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: 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