GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__Dino:3608008
          Length = 347

 Score =  298 bits (764), Expect = 1e-85
 Identities = 177/356 (49%), Positives = 223/356 (62%), Gaps = 28/356 (7%)

Query: 21  VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80
           V+ F+L I D EFLVL+GPSGCGK+TT+RM+AGLE  + G I+IGD+ V  + P+DRD+A
Sbjct: 19  VEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSGEIWIGDRMVNALDPKDRDVA 78

Query: 81  MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140
           MVFQ+Y LYP+M V EN+ F LK+    + E   RV  A+A + L +FL RKP ALSGGQ
Sbjct: 79  MVFQSYGLYPNMNVYENIRFPLKVRKVPEVEHEARVMRASAMVELDDFLHRKPAALSGGQ 138

Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200
           RQRVA+ RAIVR P VFLMDEPLSNLDAKLRV TR QI  L  +L VTT+YVTHDQ EA+
Sbjct: 139 RQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKNLSHELQVTTIYVTHDQIEAM 198

Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260
           T+ DR+ V+  G +QQVG P E+YDRPAN FVA FIGSPAMNL   +V DG  T    R+
Sbjct: 199 TLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASFIGSPAMNLMEGAVTDG--TFHGDRV 256

Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFLYGKL 320
            ++  + AA      GR+T+GFR E  +++     +D  I   +  +E LG  + +    
Sbjct: 257 AIAGLSGAA------GRVTLGFRAEDAQVV----DSDGQIAAPVYSMELLGDATMV---- 302

Query: 321 VGEGDLGSSSEDVPESGQIVVRAAPNAAPAP-GSVFHARIVEGGQHNFSASTGKRL 375
                       V   G +V   AP    A  G+    RI  G  H F A TG  L
Sbjct: 303 -----------TVKAGGTLVAVKAPKEFRAEIGAPVQIRIPTGICHLFDAQTGVHL 347


Lambda     K      H
   0.316    0.135    0.380 

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: 370
Number of extensions: 11
Number of successful extensions: 2
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: 376
Length of database: 347
Length adjustment: 29
Effective length of query: 347
Effective length of database: 318
Effective search space:   110346
Effective search space used:   110346
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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