GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Azospirillum brasilense Sp245

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AZOBR_RS25875 AZOBR_RS25875 ABC transporter ATP-binding protein

Query= TCDB::G3LHY8
         (358 letters)



>FitnessBrowser__azobra:AZOBR_RS25875
          Length = 367

 Score =  400 bits (1029), Expect = e-116
 Identities = 215/358 (60%), Positives = 255/358 (71%), Gaps = 5/358 (1%)

Query: 2   LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61
           L L   ++ VG   H+    L LERG+LNVLLGPTL+GKTSLMRLMAGLD P+ G +  D
Sbjct: 3   LVLDKVSRHVGGHVHLENVSLSLERGSLNVLLGPTLSGKTSLMRLMAGLDVPSAGRVLVD 62

Query: 62  GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121
           G DVTG  V++R+VAMVYQQFINYP+LTVY NIASP+R++ +    IDR+VR+AA LLKL
Sbjct: 63  GADVTGRHVRERSVAMVYQQFINYPSLTVYENIASPLRVARRPKDEIDRKVREAARLLKL 122

Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181
             YL RTP  LSGGQQQRTA+ARALVK A LVL+DEPLANLDYKLREELREELPKIFA +
Sbjct: 123 EAYLQRTPQQLSGGQQQRTAIARALVKEAQLVLLDEPLANLDYKLREELREELPKIFAAT 182

Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241
           GA+FVYATTEP+EALLL GNTATL +GR+ QFG T +VYRRP NL +A +F+DPPLNT+ 
Sbjct: 183 GAVFVYATTEPAEALLLRGNTATLWEGRLAQFGRTPDVYRRPANLTSARVFSDPPLNTMR 242

Query: 242 VTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSEI 301
           V K G      +G   P    LA +PD   TI F   HL L     DA  L     VSEI
Sbjct: 243 VHKRGLQIVLATGEHGPARGVLAELPDDDYTIGFRADHLHLTRPHADAIALSGAVAVSEI 302

Query: 302 TGSESFVHLEY---DG--VRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAIAA 354
           TGSESFVH++    DG   RWV +  G+ +++P   +E F+D R L  FG DGR  AA
Sbjct: 303 TGSESFVHIDLPRTDGGADRWVAVTRGVLEVEPGERIECFIDPRRLFVFGHDGRLAAA 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: 430
Number of extensions: 13
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.

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