GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Methanosarcina acetivorans C2A

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_011020340.1 MA_RS01500 ATP-binding cassette domain-containing protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_000007345.1:WP_011020340.1
          Length = 348

 Score =  204 bits (519), Expect = 3e-57
 Identities = 118/315 (37%), Positives = 188/315 (59%), Gaps = 29/315 (9%)

Query: 9   VSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRL 68
           +  + +K K  +LDN+++ +E+GE F ILGP+GAGKT F+ +IAG  VP +G +  D + 
Sbjct: 4   IESLSRKWKNFSLDNLSLKVESGEYFVILGPTGAGKTLFLELIAGFHVPDSGRILLDGKD 63

Query: 69  VASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKIL 128
           V       + PE   I  V+Q ++L+P++   +N+ F    M+M K +  KRV + A+ L
Sbjct: 64  VTD-----LSPEKHDIAFVYQNYSLFPHMNVKKNLEF---GMRMKKIKDPKRVLDTARDL 115

Query: 129 DIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQS 188
            I H+L+  P  LSGG+QQRVALARALV +P +LLLDEP S LD R +++AR ++  +  
Sbjct: 116 KIEHLLDRNPLTLSGGEQQRVALARALVTNPKILLLDEPLSALDPRTQENAREMLSVLHK 175

Query: 189 RLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELE 248
           +  +T+L ++HD  +   +ADR+ V++ GKL+QVGKPE++++ PV  +VAS +G  N L+
Sbjct: 176 KNKLTVLHITHDQTEARIMADRIAVVMDGKLIQVGKPEEIFEKPVEGRVASFVGFENVLK 235

Query: 249 GKVTNE---------GVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKD--------- 290
           G+V +          G V+      + V  D+    +RPE++ LSK   +          
Sbjct: 236 GRVISAEQGLLRIRVGEVVIDAAGDMEV-GDQVYAFLRPENIALSKSSTQSSIRNSLQGR 294

Query: 291 --DSWILVGKGKVKV 303
             ++W+L    +VKV
Sbjct: 295 VTEAWVLGALVRVKV 309


Lambda     K      H
   0.319    0.139    0.390 

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: 18
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: 353
Length of database: 348
Length adjustment: 29
Effective length of query: 324
Effective length of database: 319
Effective search space:   103356
Effective search space used:   103356
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 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