GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Cupriavidus basilensis 4G11

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein

Query= TCDB::G3LHY8
         (358 letters)



>FitnessBrowser__Cup4G11:RR42_RS18590
          Length = 359

 Score =  182 bits (463), Expect = 9e-51
 Identities = 115/355 (32%), Positives = 183/355 (51%), Gaps = 12/355 (3%)

Query: 2   LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61
           +++R   K  G+   I   D+ +  G   VL+GP+  GK++L+R++AGL+  T G I   
Sbjct: 4   VQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEIAIG 63

Query: 62  GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121
              V  +P ++R++AMV+Q +  YP +TVY+N+A  ++++  D   I R+V KA+ +L L
Sbjct: 64  NRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAILGL 123

Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181
              L+R P  LSGGQ+QR A+ RA+V++  + L DEPL+NLD KLR ++R E+ ++  + 
Sbjct: 124 DSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELHQRL 183

Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241
               VY T +  EA+ +      +  GRV Q G  + +Y  P NL  AG    P +N + 
Sbjct: 184 RTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAMNFVP 243

Query: 242 --VTKSGN--VFTRPSGVTIPVPSHLAVV--PDGP-VTIAFHPHHLGLA-PQTGDAARLQ 293
             + +SG       P G  +P P+        DG  V     P HL L  P  G    LQ
Sbjct: 244 GVLRRSGGDAAVEFPDGTRLPAPARFDATAGTDGQRVIYGVRPEHLTLGMPGQG----LQ 299

Query: 294 ARTLVSEITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSD 348
            R  V E TG+ + ++  +    ++ +    HD      +    D +H   F +D
Sbjct: 300 TRVSVVEPTGANTEIYSRFCEAEFISIFRERHDFAAGDILNLVPDHQHTHLFDAD 354


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: 296
Number of extensions: 9
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: 359
Length adjustment: 29
Effective length of query: 329
Effective length of database: 330
Effective search space:   108570
Effective search space used:   108570
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