GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Dyella japonica UNC79MFTsu3.2

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4212
          Length = 364

 Score =  298 bits (763), Expect = 2e-85
 Identities = 169/358 (47%), Positives = 225/358 (62%), Gaps = 8/358 (2%)

Query: 1   MADLKLTGVEKAYGDVKV-LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGT 59
           MA ++L  + K Y +  V ++  + +I  GEL+V VGPSGCGK+TLLRMIAGLE I+GGT
Sbjct: 1   MAKVRLDKLRKVYPNGHVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGT 60

Query: 60  LEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAE 119
           L I   VVND+ P  R IAMVFQ+YALYPHMTV EN+ F LK+  + +AEI+  V  AA 
Sbjct: 61  LSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAAR 120

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            L+L Q LD  P ALSGGQRQRVA+GR++VRDPKV+L DEPLSNLDA LR++ R+EIA++
Sbjct: 121 MLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARI 180

Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239
            + + ++TMVYVTHDQ+EAMTL  RIVVL GG I Q+ +P+ LY+ P N FVA F+GSP 
Sbjct: 181 HQRL-KATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPA 239

Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSL---MGAAVNVGVRPEDMVEAAPGGD 296
           MNLL G +   G    + M  G   + + P   +L       + VG+RPED++  A    
Sbjct: 240 MNLLRGILYRDGG-WKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLLLCADAAG 298

Query: 297 YVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
                ++ + E +G    L      GE   + ++        G        P ++H F
Sbjct: 299 AALAAQLEVVEPVGNEVFLNLR--HGELALVSRMPPRELPAPGSTLHFGFAPERLHFF 354


Lambda     K      H
   0.316    0.135    0.379 

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: 429
Number of extensions: 21
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: 373
Length of database: 364
Length adjustment: 30
Effective length of query: 343
Effective length of database: 334
Effective search space:   114562
Effective search space used:   114562
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