GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Methanosarcina acetivorans C2A

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_011020340.1 MA_RS01500 ATP-binding cassette domain-containing protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_000007345.1:WP_011020340.1
          Length = 348

 Score =  173 bits (438), Expect = 7e-48
 Identities = 101/270 (37%), Positives = 157/270 (58%), Gaps = 9/270 (3%)

Query: 19  LSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPAQRGIA 78
           L N++L ++ GE  V +GP+G GK+  L +IAG      G + +DG  V D+ P +  IA
Sbjct: 16  LDNLSLKVESGEYFVILGPTGAGKTLFLELIAGFHVPDSGRILLDGKDVTDLSPEKHDIA 75

Query: 79  MVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKALSGGQ 138
            V+Q+Y+L+PHM V++N+ F +++ K    +    V   A  L++   LDR P  LSGG+
Sbjct: 76  FVYQNYSLFPHMNVKKNLEFGMRMKKIKDPK---RVLDTARDLKIEHLLDRNPLTLSGGE 132

Query: 139 RQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTHDQVEA 198
           +QRVA+ R++V +PK+ L DEPLS LD   +   R E+  +     + T++++THDQ EA
Sbjct: 133 QQRVALARALVTNPKILLLDEPLSALDPRTQENAR-EMLSVLHKKNKLTVLHITHDQTEA 191

Query: 199 MTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQTTVEM 258
             +A RI V+  G + QVG P E++EKP    VA F+G    N+L G++I   A+  +  
Sbjct: 192 RIMADRIAVVMDGKLIQVGKPEEIFEKPVEGRVASFVGFE--NVLKGRVI--SAEQGLLR 247

Query: 259 TDGGRAVSDYPSDDSLMGAAVNVGVRPEDM 288
              G  V D  + D  +G  V   +RPE++
Sbjct: 248 IRVGEVVID-AAGDMEVGDQVYAFLRPENI 276


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: 305
Number of extensions: 15
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: 348
Length adjustment: 29
Effective length of query: 344
Effective length of database: 319
Effective search space:   109736
Effective search space used:   109736
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