GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Pseudomonas fluorescens GW456-L13

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate PfGW456L13_3039 Various polyols ABC transporter, ATP-binding component

Query= TCDB::G3LHY8
         (358 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3039
          Length = 367

 Score =  196 bits (498), Expect = 8e-55
 Identities = 124/360 (34%), Positives = 193/360 (53%), Gaps = 13/360 (3%)

Query: 2   LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61
           L+++N  K       I   DL +      V +GP+  GK++L+RL+AGL+  +GG+I  D
Sbjct: 4   LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELD 63

Query: 62  GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121
           G D+T +   KR++AMV+Q +  YP ++V  N++  + ++G   A ++++V +AA +L+L
Sbjct: 64  GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILEL 123

Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181
            P L+R P  LSGGQ+QR A+ RA+V+N  + L DEPL+NLD  LR ++R EL ++  + 
Sbjct: 124 GPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKEL 183

Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241
            A  +Y T +  EA+ +      LN G++ Q G  +++Y +P NL  AG    P +  L 
Sbjct: 184 QATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLK 243

Query: 242 -----VTKSGNVFTRPSGVTIPVP---SHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQ 293
                V   G      +G  + +P    HL+V     VT+   P HL LA + GD A LQ
Sbjct: 244 GKITRVDSQGCEVQLDAGTRVSLPLGGRHLSV--GSAVTLGIRPEHLELA-KPGDCA-LQ 299

Query: 294 ARTLVSEITGSESFVHLE-YDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAI 352
               VSE  GS++F H+    G    M   G         +   LD +H   F +DG A+
Sbjct: 300 VTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFDADGVAL 359


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: 311
Number of extensions: 14
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: 367
Length adjustment: 29
Effective length of query: 329
Effective length of database: 338
Effective search space:   111202
Effective search space used:   111202
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