GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Marinobacter adhaerens HP15

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF3902 HP15_3842 iron(III) ABC transporter, ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Marino:GFF3902
          Length = 371

 Score =  207 bits (526), Expect = 5e-58
 Identities = 116/264 (43%), Positives = 162/264 (61%), Gaps = 6/264 (2%)

Query: 23  NVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIVPPEDR 82
           ++N+++E GE   +LGPSG GKTT +RI AGL +P+ G+++    LV++ G + VPPE R
Sbjct: 40  DINLHLEAGEVVCLLGPSGCGKTTLLRIAAGLQMPTRGKVFLGSSLVSAPGGVQVPPEKR 99

Query: 83  KIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHFPRELS 142
            +G+ FQ  AL+P+LT  EN+ F +++M   K++ R R  E+   L +    N +P  LS
Sbjct: 100 NVGLAFQESALFPHLTVLENVCFGISSMP--KKQQRTRALELLGRLGMADAANVYPHTLS 157

Query: 143 GGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSHDPA 202
           GGQQQRVALARAL   P ++LLDEPFS+LDAR+RD  R     V   L    L+V+HDP 
Sbjct: 158 GGQQQRVALARALAPSPRVMLLDEPFSSLDARLRDQIRDDTLHVLKELNTATLLVTHDPE 217

Query: 203 DIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVTNEGVV---IG 259
           +   +ADR+ ++  G++VQ G P DLY NP    V +  G++NE  G V N GVV   +G
Sbjct: 218 EAMFMADRIALMRDGEIVQTGTPTDLYCNPAEPFVVNFFGQVNEHRGVVHN-GVVTTPLG 276

Query: 260 SLRFPVSVSSDRAIIGIRPEDVKL 283
            L            I IRPE VK+
Sbjct: 277 HLEAKGFEDGSSVRILIRPEAVKV 300


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: 316
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: 353
Length of database: 371
Length adjustment: 29
Effective length of query: 324
Effective length of database: 342
Effective search space:   110808
Effective search space used:   110808
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 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:

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