GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpS in Phaeobacter inhibens BS107

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF1302 PGA1_c13180 ABC transporter, ATP binding protein

Query= TCDB::G3LHY8
         (358 letters)



>lcl|FitnessBrowser__Phaeo:GFF1302 PGA1_c13180 ABC transporter, ATP
           binding protein
          Length = 334

 Score =  201 bits (510), Expect = 3e-56
 Identities = 128/354 (36%), Positives = 181/354 (51%), Gaps = 27/354 (7%)

Query: 2   LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61
           ++L +  K  G    I P DL +E G   V +GP+  GK++L+RL+AGL+  T G+I  D
Sbjct: 4   IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63

Query: 62  GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121
           G D T +P  KR +AMV+Q +  YP ++V  NIA PM+++G  A    R +  AA  L L
Sbjct: 64  GEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123

Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181
           T YLDR P  LSGGQ+QR A+ RA+V+  +  L DEPL+NLD  LR  +R E+ ++  + 
Sbjct: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183

Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241
               +Y T +  EA+ +      L  G + Q G  +E+YR P N+  AG    P +N L 
Sbjct: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLL- 242

Query: 242 VTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTL-VSE 300
                   T P         H A       TI   P HL ++   G    + A T+ VSE
Sbjct: 243 --------TGPQAA-----QHNA------ATIGIRPEHLSISETEG----MWAGTIGVSE 279

Query: 301 ITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFL--DTRHLMAFGSDGRAI 352
             GS++F H++ D     +      ++D       FL  D  HL  FGSDG  I
Sbjct: 280 HLGSDTFFHVQCDAFDDPLTVRASGELDLGYGERVFLTPDMTHLHRFGSDGLRI 333


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: 325
Number of extensions: 14
Number of successful extensions: 3
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: 334
Length adjustment: 29
Effective length of query: 329
Effective length of database: 305
Effective search space:   100345
Effective search space used:   100345
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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