GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Phaeobacter inhibens BS107

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF3390 PGA1_c34430 putrescine transport ATP-binding protein PotG

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Phaeo:GFF3390
          Length = 375

 Score =  202 bits (514), Expect = 1e-56
 Identities = 112/317 (35%), Positives = 187/317 (58%), Gaps = 23/317 (7%)

Query: 7   KNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDD 66
           +NV+K F  G+  A+D++ + I   E F +LGPSG GKTT MR++AG + P+ G+++   
Sbjct: 21  QNVTKRF--GEFTAIDDLTLGIYEKEFFALLGPSGCGKTTMMRMLAGFETPTEGKIFLSG 78

Query: 67  RLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAK 126
           + +A      VPP  R + M+FQ++AL+P+L+ ++NIAF L      K +I +RV+E+ +
Sbjct: 79  QDIAP-----VPPNKRLVNMMFQSYALFPHLSVWDNIAFGLKRENKPKHDIAERVQEMLR 133

Query: 127 ILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEV 186
           +  +       P ++SGGQ+QRVALAR+L K P LLLLDEP   LD ++R   +  + ++
Sbjct: 134 LTRLEKFARRKPHQISGGQRQRVALARSLAKAPKLLLLDEPLGALDKKLRQDTQFELMDI 193

Query: 187 QSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINE 246
           Q + G T ++V+HD  +   +A RV V+  G++VQV  P+ +Y+ P S+ VA  IG++N 
Sbjct: 194 QEKTGTTFVIVTHDQEEAMTVASRVAVMDNGRIVQVATPDRIYETPNSLYVADFIGDVNI 253

Query: 247 LEGKVTNEGVVIGSLRF-----PVSVSSDRAI-------IGIRPEDVKLSKD-VIKDDSW 293
           + G  T  G    ++ +     P++V S  +        + IRPE V +S +   + D+ 
Sbjct: 254 IGGTATPTGPEQYAVNWKDGAAPLTVKSQASFSDGQECHLAIRPEKVTISAERPAEADNT 313

Query: 294 ILVGKGKVKVIGYQGGL 310
           +   +G++  I Y G +
Sbjct: 314 V---QGRILDIAYLGNI 327


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: 295
Number of extensions: 18
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: 375
Length adjustment: 29
Effective length of query: 324
Effective length of database: 346
Effective search space:   112104
Effective search space used:   112104
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.

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 (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