GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Pseudomonas fluorescens FW300-N2E3

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate AO353_29310 AO353_29310 transporter

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_29310
          Length = 380

 Score =  204 bits (518), Expect = 4e-57
 Identities = 116/319 (36%), Positives = 180/319 (56%), Gaps = 21/319 (6%)

Query: 5   IVKNVSKVFKK-GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           ++  V +V KK  + +A+D+V+++I  GE F +LG SG+GK+T +R++AG + P+ G +Y
Sbjct: 21  VLVRVDRVTKKFDETIAVDDVSLDIHQGEIFAMLGGSGSGKSTLLRMLAGFERPTEGRIY 80

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123
            D   +       +PP +R I M+FQ++AL+P++T  +NIAF L   ++   EI  RVEE
Sbjct: 81  LDGVDITD-----MPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDRLPASEIEARVEE 135

Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183
           + K++ +       P +LSGGQ+QRVALAR+L K P LLLLDEP   LD ++R   +  +
Sbjct: 136 MLKLVHMTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLEL 195

Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243
            E+  R+GVT ++V+HD  +   +A R+ ++  G + Q+G P D+Y+ PVS  V   IG 
Sbjct: 196 VEIIERVGVTCVMVTHDQEEAMTMAQRIAIMHLGWIAQIGSPVDIYEAPVSRMVCEFIGN 255

Query: 244 INELEGKVTNEGVVIGSLRFP-------------VSVSSDRAIIGIRPEDVKLSKDVIKD 290
           +N  +G V  +      +  P              SV        IRPE  K+    +K 
Sbjct: 256 VNAFDGTVVEDLEGHAIIHSPDLEQKIYVGHGVSTSVQDKSITYAIRPE--KMLVSTLKP 313

Query: 291 DSWILVGKGKVKVIGYQGG 309
           D+     +GKV  I Y GG
Sbjct: 314 DTRYNWSQGKVHDIAYLGG 332


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: 297
Number of extensions: 11
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 353
Length of database: 380
Length adjustment: 30
Effective length of query: 323
Effective length of database: 350
Effective search space:   113050
Effective search space used:   113050
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