GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Desulfacinum hydrothermale DSM 13146

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_084058299.1 B9A12_RS12455 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_900176285.1:WP_084058299.1
          Length = 367

 Score =  160 bits (406), Expect = 4e-44
 Identities = 113/358 (31%), Positives = 176/358 (49%), Gaps = 9/358 (2%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           L L  V++       L ++ L+   G   + +G +  GK+TLLR++AGL++ T G + +D
Sbjct: 3   LTLEHVDRIVDGETHLCDVTLEFPSGSRNILLGRTLAGKTTLLRIMAGLDRPTRGRVLVD 62

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123
           G  V  V   +R +AMV+Q +  YP  TV +N++  L++    + EID  V   AE L+L
Sbjct: 63  GKDVTGVSVRKRNVAMVYQQFINYPSFTVYDNIASPLRLQGVPREEIDRRVREVAEMLRL 122

Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183
              LDRLP  LSGGQ+QR AI R++V+D  + L DEPL NLD  LR   R E+  + E  
Sbjct: 123 TPLLDRLPAQLSGGQQQRTAIARALVKDADLLLLDEPLVNLDYKLREELREELTAIFE-R 181

Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243
             S +VY T +  EA+ L   +V+L  G + Q G   ++Y +P     A+    P +N L
Sbjct: 182 GRSIVVYTTTEPTEALMLGGNVVILDEGRVLQTGPTDQVYHRPTTMRAAEVYSDPPINYL 241

Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPED-MVEAAPGGDYVFEGK 302
              + G+ A+   ++T    A       + L     + G+R     ++     D   E +
Sbjct: 242 DLVVEGSQARIGEQVTFALCA-----HLEGLAPGRYHAGLRANRFFLKRRTDRDVALESQ 296

Query: 303 VAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVFKDGVSL 360
           V ++E  G  T ++        P +    GI     G    + A+PA+  VF    SL
Sbjct: 297 VELSEINGSETFIHVNHQG--FPLVVHETGIRTYKMGSTVTVHADPAQFFVFNQEGSL 352


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: 325
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: 373
Length of database: 367
Length adjustment: 30
Effective length of query: 343
Effective length of database: 337
Effective search space:   115591
Effective search space used:   115591
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 Apr 09 2024. 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