GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Pseudomonas fluorescens FW300-N2E3

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AO353_25895 AO353_25895 ABC transporter ATP-binding protein

Query= TCDB::G3LHY8
         (358 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25895
          Length = 367

 Score =  199 bits (505), Expect = 1e-55
 Identities = 126/359 (35%), Positives = 191/359 (53%), Gaps = 9/359 (2%)

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

Query: 62  GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121
           G D+T +   KR++AMV+Q +  YP ++V  N++  + ++G + A ++++V +AA +L+L
Sbjct: 64  GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARILEL 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 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241
            A  +Y T +  EA+ L      LN GR+ Q G  +E+Y +P NL  AG    P +  L 
Sbjct: 184 QATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLK 243

Query: 242 -----VTKSGNVFTRPSGVTIPVP-SHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQAR 295
                V +        +G  I +P S   +   G VT+   P HL LA   GD   LQ  
Sbjct: 244 GKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLA-LPGDCT-LQVT 301

Query: 296 TLVSEITGSESFVH-LEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAIA 353
             VSE  GS++F H L   G    M   G        ++   LD  H   F ++G A+A
Sbjct: 302 ADVSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDANGVAVA 360


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: 307
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:

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