GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Dyella japonica UNC79MFTsu3.2

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4212
          Length = 364

 Score =  311 bits (798), Expect = 1e-89
 Identities = 180/374 (48%), Positives = 233/374 (62%), Gaps = 23/374 (6%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MA V        YP      V + + EIADGE LVLVGPSGCGK+T LRM+AGLE+++ G
Sbjct: 1   MAKVRLDKLRKVYPNG-HVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            + IG++ V  +AP+DRDIAMVFQNYALYPHMTV EN+GF LK+ G+ + EI +RV EAA
Sbjct: 60  TLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAA 119

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             L L + L+ +P ALSGGQRQRVA+GRA+VR+P+VFL+DEPLSNLDAKLR+  R +IA 
Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           + ++L  T VYVTHDQ EA+T+G RI VL  G +QQ+  P  LYD PAN+FVAGF+GSPA
Sbjct: 180 IHQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPA 239

Query: 241 MN-LGTFSVKDGD----ATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGES 295
           MN L     +DG        G   +   P+  A     D   I +G RPE L +    ++
Sbjct: 240 MNLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDRD-IVVGLRPEDLLLC--ADA 296

Query: 296 TDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVF 355
              ++  +L+ VE +G++ FL    +  G+L            +V R  P   PAPGS  
Sbjct: 297 AGAALAAQLEVVEPVGNEVFLN---LRHGELA-----------LVSRMPPRELPAPGSTL 342

Query: 356 HARIVEGGQHNFSA 369
           H        H F A
Sbjct: 343 HFGFAPERLHFFDA 356


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: 400
Number of extensions: 13
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: 376
Length of database: 364
Length adjustment: 30
Effective length of query: 346
Effective length of database: 334
Effective search space:   115564
Effective search space used:   115564
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