GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Flavobacterium ummariense DS-12

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_091524012.1 BM253_RS11210 ABC transporter ATP-binding protein

Query= TCDB::Q88P35
         (384 letters)



>NCBI__GCF_900115115.1:WP_091524012.1
          Length = 312

 Score =  117 bits (294), Expect = 3e-31
 Identities = 89/334 (26%), Positives = 160/334 (47%), Gaps = 49/334 (14%)

Query: 4   LELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAIL 63
           L++  ++ +Y +     L D+   +K G    L+G SG GKSTL+  + GL     G+I 
Sbjct: 2   LQVNQLSFSYNNS--QILSDVSFQLKAGNSYALIGASGSGKSTLLKLVYGLLDADSGSIF 59

Query: 64  IDEQDVSG----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARV 119
            +E+ + G    + P    +  + Q + L P +SV EN+      R L    + E+  RV
Sbjct: 60  WNEKQILGPAYHLVPGMDYMKYLAQDFDLMPFVSVAENVG-----RFLSNFYLKEKKNRV 114

Query: 120 AKLLQIEHLLAR---KPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176
            +LL++  +      K   LSGGQ QR A+ R LA  P+  L DEP S++D   + E+ T
Sbjct: 115 DELLELVDMTEFANVKAKFLSGGQMQRTALARVLALEPEFLLLDEPFSHIDPFQKRELAT 174

Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFI 236
           ++    ++   T ++ +H   EA+   D++ V+++GI+ +   PQ IY +P N+++A   
Sbjct: 175 QLFQYCKQKGITILFTSHTPEEALMYADEILVLQNGILIEKDIPQNIYENPKNEYIARLT 234

Query: 237 GSPPMNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQIALGAA 296
           G   +N IP                     +L + E          +L +RP ++ + + 
Sbjct: 235 GD--VNIIPANY-----------------FDLNINE----------VLYVRPHELQI-SN 264

Query: 297 DGNGLPAIRAEVQVTEPTGPDLLVFVTLNQTKVC 330
           DG+       +++ +  TG + L++  LN  ++C
Sbjct: 265 DGS-----EVKIKHSYFTGKNYLIYAVLNDLEIC 293


Lambda     K      H
   0.320    0.137    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: 233
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: 384
Length of database: 312
Length adjustment: 29
Effective length of query: 355
Effective length of database: 283
Effective search space:   100465
Effective search space used:   100465
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 24 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