GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglK' in Sphingomonas koreensis DSMZ 15582

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Ga0059261_3668 Ga0059261_3668 ABC transporter

Query= uniprot:A8LLL2
         (373 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_3668 Ga0059261_3668 ABC
           transporter
          Length = 201

 Score =  119 bits (299), Expect = 5e-32
 Identities = 78/207 (37%), Positives = 115/207 (55%), Gaps = 23/207 (11%)

Query: 9   VEKAYGDVKVLSNINLDIQQGE-LIVFVGPSGCGKSTLLRMIAGLEKI------TGGTLE 61
           +EK  GD +    I+  I+ GE +IV  GPSG GK+++L M+AGL +        GG   
Sbjct: 7   IEKRRGDAQ----ISCRIEGGEGIIVLFGPSGVGKTSVLDMVAGLLEPDTGHVRVGGETL 62

Query: 62  IDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKL 121
            D  +  DVPP +R    VFQ   L+PH++VR N+ +          ++       A + 
Sbjct: 63  FDAAIGEDVPPERRRAGYVFQDARLFPHLSVRANLLYGAGGDPSGLGDL-------AARF 115

Query: 122 QLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKE 181
            +   LDR P++LSGG+ +RVAIGR+++  P+  L DEPLS+LD A R      I +L++
Sbjct: 116 DIAHLLDRWPRSLSGGEARRVAIGRALLAKPRFLLLDEPLSSLDRARREEVTRVIERLRD 175

Query: 182 --AMPESTMVYVTHDQVEAMTLATRIV 206
             A+P   ++ VTHD VEA  L  RI+
Sbjct: 176 EAALP---ILMVTHDPVEAERLGQRII 199


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: 211
Number of extensions: 11
Number of successful extensions: 4
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: 201
Length adjustment: 25
Effective length of query: 348
Effective length of database: 176
Effective search space:    61248
Effective search space used:    61248
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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