GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Sinorhizobium fredii NGR234

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000018545.1:WP_164924745.1
          Length = 355

 Score =  333 bits (854), Expect = 5e-96
 Identities = 180/365 (49%), Positives = 244/365 (66%), Gaps = 12/365 (3%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           M D+  + + K Y G   V+  L   I DGEFVVL+GPSGCGKST+LRM+AGLE+ISGG 
Sbjct: 1   MTDVTIRNVTKRY-GALTVIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGGD 59

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           L +G  V+ND PA+ER++A+VFQNYALYPHM+V +N+ F L+  KRP AEID RV + AA
Sbjct: 60  LLMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKRPRAEIDERVDKAAA 119

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
           +L L  LL+R PRA+SGGQ+QR A+ RAI++ P VFLFDEPLSNLDAKLR Q+R +IK L
Sbjct: 120 ILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKAL 179

Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240
           HQRL+ TTVYVTHDQ+EAMT+AD++++M +GR+ Q G+P ELY  P N+F AGFIG+P+M
Sbjct: 180 HQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPSM 239

Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300
           NFL  TV   +G L      +  AL  +    L     V   +RP+H+++          
Sbjct: 240 NFLPATVAATNGPLL--KTPEGVALPIDGGPTLTGRSEVTYGIRPEHLQL-------GET 290

Query: 301 TCPVSVELVEILGADALLTTRCGDQTLTALVPADRLP-QPGATLTLALDQHELHVFDVES 359
             P  V +VE  G++  L    G + + A++  DR+  +PG  + L   +   H+FD  +
Sbjct: 291 GIPAEVVVVEPTGSETQLYVTVGGREVVAVL-RDRVDVRPGEKIWLTPRKGCAHLFDPNT 349

Query: 360 GENLS 364
           G  ++
Sbjct: 350 GARIA 354


Lambda     K      H
   0.321    0.137    0.403 

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: 394
Number of extensions: 15
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: 406
Length of database: 355
Length adjustment: 30
Effective length of query: 376
Effective length of database: 325
Effective search space:   122200
Effective search space used:   122200
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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