GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_29310 AO353_29310
           transporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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