GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Marivita geojedonensis DPG-138

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  288 bits (736), Expect = 2e-82
 Identities = 154/364 (42%), Positives = 223/364 (61%), Gaps = 16/364 (4%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           M+ +  +++ K Y G   V+H +DL + DGEF V +GPSGCGKST+LRM+AGLE+ + GT
Sbjct: 1   MSGVTLESVIKRY-GQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGT 59

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           +RIGG  V  L   +R V+MVFQ YALYPHM+V +N+ FGL+     A +I  +V E + 
Sbjct: 60  IRIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASR 119

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
           +L L+  L+RKP+A+SGGQ+QR AI RAI++ P VFLFDEPLSNLDA+LR ++R +I RL
Sbjct: 120 ILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARL 179

Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240
           H+ +  T +YVTHDQ+EAMTLAD++++++ GRI Q G+P ELYR P N F AGFIG+P+M
Sbjct: 180 HKEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSM 239

Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300
           NF+ G VQ        E        +  + +  +    V + +RP+H+ +         L
Sbjct: 240 NFIRGRVQGG------EVVSDGLVHSVSKTASAQEGQEVLIGLRPEHLELRPGSSHRVDL 293

Query: 301 TCPV-SVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVES 359
           T  +  V    ++G D         + +      D     G  + L +D   + +FD ++
Sbjct: 294 TESLGGVSYAHLIGPDG--------EKIIVEERGDHRSSDGDMVDLVVDPDHMFLFDAKT 345

Query: 360 GENL 363
              L
Sbjct: 346 EARL 349


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: 362
Number of extensions: 13
Number of successful extensions: 1
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: 350
Length adjustment: 30
Effective length of query: 376
Effective length of database: 320
Effective search space:   120320
Effective search space used:   120320
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 24 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