GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK_Bb in Dyella japonica UNC79MFTsu3.2

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate N515DRAFT_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein

Query= uniprot:Q6MNM2
         (347 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4212 N515DRAFT_4212 multiple
           sugar transport system ATP-binding protein
          Length = 364

 Score =  295 bits (756), Expect = 9e-85
 Identities = 164/329 (49%), Positives = 208/329 (63%), Gaps = 28/329 (8%)

Query: 1   MAKIQFSNIKKSFGSADV-LKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59
           MAK++   ++K + +  V +     +IA GE LVLVGPSGCGK+TLLR +AGLES   GT
Sbjct: 1   MAKVRLDKLRKVYPNGHVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGGT 60

Query: 60  ISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISE 119
           +SI  + +NDI P++RDIAMVFQ+YALYPHMTVAEN+GFGLKL+    AEI +RV E + 
Sbjct: 61  LSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAAR 120

Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179
           +L+++  LD +P  LSGGQRQRVALGRAL R   V L DEPLSNLDA LR  MR+EI R+
Sbjct: 121 MLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIARI 180

Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239
           H   K+TM+YVTHDQ+EA TLG RI VL  GVI+QI TP  +Y  P N F+A F+GSP M
Sbjct: 181 HQRLKATMVYVTHDQIEAMTLGQRIVVLNGGVIQQIDTPMNLYDTPANLFVAGFLGSPAM 240

Query: 240 NFLEGAVLEKIPWPEA--------------------RKADQILGIRPDAFALNQGPLGTQ 279
           N L G +     W  A                    R  D ++G+RP+   L     G  
Sbjct: 241 NLLRGILYRDGGWKLAMPQGELVLGELPQGAALEAWRDRDIVVGLRPEDLLLCADAAGAA 300

Query: 280 EVALGDFQIDISENLGGQQML---HGTLA 305
             A    Q+++ E +G +  L   HG LA
Sbjct: 301 LAA----QLEVVEPVGNEVFLNLRHGELA 325


Lambda     K      H
   0.318    0.136    0.383 

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: 343
Number of extensions: 12
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: 347
Length of database: 364
Length adjustment: 29
Effective length of query: 318
Effective length of database: 335
Effective search space:   106530
Effective search space used:   106530
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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