GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Marivita geojedonensis DPG-138

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::G3LHY8
         (358 letters)



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  188 bits (478), Expect = 2e-52
 Identities = 117/349 (33%), Positives = 178/349 (51%), Gaps = 8/349 (2%)

Query: 4   LRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGT 63
           L +  K  G    I+  DL ++ G   V +GP+  GK++L+R++AGL+  T G+I   G 
Sbjct: 6   LESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTIRIGGR 65

Query: 64  DVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTP 123
           DVT +    R V+MV+Q +  YP +TV  N+   ++++G  A  I  +V +A+ +LKL  
Sbjct: 66  DVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRILKLDD 125

Query: 124 YLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGA 183
           YL R P  LSGGQ+QR A+ RA+V+   + L DEPL+NLD +LR E+R E+ ++  + GA
Sbjct: 126 YLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLHKEIGA 185

Query: 184 IFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDVT 243
             +Y T +  EA+ L      L  GR+ Q G  +E+YR P N   AG    P +N +   
Sbjct: 186 TMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMNFIRGR 245

Query: 244 KSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSEITG 303
             G       G+   V    +      V I   P HL L P  G + R+     ++E  G
Sbjct: 246 VQGGEVV-SDGLVHSVSKTASAQEGQEVLIGLRPEHLELRP--GSSHRVD----LTESLG 298

Query: 304 SESFVHL-EYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRA 351
             S+ HL   DG + ++   G H       V+  +D  H+  F +   A
Sbjct: 299 GVSYAHLIGPDGEKIIVEERGDHRSSDGDMVDLVVDPDHMFLFDAKTEA 347


Lambda     K      H
   0.319    0.136    0.392 

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: 306
Number of extensions: 8
Number of successful extensions: 1
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: 358
Length of database: 350
Length adjustment: 29
Effective length of query: 329
Effective length of database: 321
Effective search space:   105609
Effective search space used:   105609
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 24 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