GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpS in Pseudomonas fluorescens FW300-N2E2

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Pf6N2E2_807 Various polyols ABC transporter, ATP-binding component

Query= TCDB::G3LHY8
         (358 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_807 Various polyols ABC
           transporter, ATP-binding component
          Length = 367

 Score =  198 bits (503), Expect = 2e-55
 Identities = 125/361 (34%), Positives = 191/361 (52%), Gaps = 9/361 (2%)

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

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

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

Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTL- 240
            A  +Y T +  EA+ L      LN GR+ Q G  +E+Y +P NL  AG    P +  L 
Sbjct: 184 QATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLK 243

Query: 241 ----DVTKSGNVFTRPSGVTIPVP-SHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQAR 295
                +   G      +G  I +P S   +   G VT+   P HL LA Q GD   LQ  
Sbjct: 244 GKVTGLDSQGCEVLLDAGTRINLPRSGANLSVGGAVTLGIRPEHLNLA-QPGDCT-LQVT 301

Query: 296 TLVSEITGSESFVH-LEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAIAA 354
             VSE  GS++F H +   G    M   G        ++   LD  H   F ++G A+  
Sbjct: 302 ADVSERLGSDTFCHVVTASGEALTMRVRGDLASRFGEQLSLHLDAEHCHLFDAEGVAVTR 361

Query: 355 A 355
           A
Sbjct: 362 A 362


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: 14
Number of successful extensions: 2
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.

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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 paper from 2022 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