GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Sinorhizobium meliloti 1021

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate SM_b20235 SM_b20235 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__Smeli:SM_b20235
          Length = 363

 Score =  314 bits (804), Expect = 3e-90
 Identities = 171/360 (47%), Positives = 229/360 (63%), Gaps = 24/360 (6%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           MA +  + + K + G   V+H +   I DGEFV L+GPSGCGKST+LRMIAGLE+IS G 
Sbjct: 1   MASVEIRNVVKRF-GALEVVHGVSAEIADGEFVALVGPSGCGKSTLLRMIAGLEEISDGA 59

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           + IGG +VN++  ++RN++MVFQNYALYPHM+V +N+AF LR  + P  E  R+V E A 
Sbjct: 60  VVIGGDIVNEVAPKDRNISMVFQNYALYPHMTVAENMAFALRLARLPKDEQKRKVGEAAT 119

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

Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240
           HQRLRTT++YVTHDQ+EAMT+ADR+++M+DG + Q G+P E++ YPRNLF A FIG+P+M
Sbjct: 180 HQRLRTTSIYVTHDQIEAMTMADRIVVMRDGNVEQIGTPLEIFDYPRNLFVASFIGSPSM 239

Query: 241 NFLSGTVQ----RQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREP 296
           NF+ G V     R  G + I                L H       +RP+ ++I G   P
Sbjct: 240 NFIEGEVVGGTFRAPGGIIIPAPD------------LAHKGPTVAGIRPNKLQI-GATGP 286

Query: 297 AASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFD 356
           +A       V +VE  G +  L    G   L  L+       PG  + LA    ++H FD
Sbjct: 287 SA------KVLIVEPTGDETHLLVELGGAQLAMLLRERTSLAPGDEIGLAFASADVHFFD 340


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: 437
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: 363
Length adjustment: 30
Effective length of query: 376
Effective length of database: 333
Effective search space:   125208
Effective search space used:   125208
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 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