GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Brucella inopinata BO1

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000182725.1:WP_008510542.1
          Length = 333

 Score =  274 bits (701), Expect = 2e-78
 Identities = 157/362 (43%), Positives = 216/362 (59%), Gaps = 33/362 (9%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           M  +  +++ K Y G   VL  ++L + DGEF++ +GPSGCGKST+LR IAGLED+S G 
Sbjct: 1   MGSLQLKSVHKRY-GAQEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAGQ 59

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           + I G  V   P   R +AMVFQ+YALYPH++V  N+  GL++   P  EI+ RV + +A
Sbjct: 60  VLINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKASA 119

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
           +L LE  L R+P  +SGGQ+QR AI RA+++ P +FLFDEPLSNLDA LR Q R +I +L
Sbjct: 120 MLALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAKL 179

Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240
           H+ L+ T +YVTHDQ+EAMTLADR++++  GRI Q GSP ELY  P NLF AGFIG+P M
Sbjct: 180 HRELKATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQM 239

Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300
           NF+                  R   TG R           + +RP+H+ ++ E     S 
Sbjct: 240 NFIEAA---------------RIGATGAR----------TIGIRPEHLSVSRE-----SG 269

Query: 301 TCPVSVELVEILGADALLTTRCGDQTL-TALVPADRLPQPGATLTLALDQHELHVFDVES 359
           T    V   E LGAD +L        L TA +  ++       + L  ++ + H FD E+
Sbjct: 270 TWKGKVIHAEHLGADTILYVETETAGLVTARLFGEQHYNEDDVIFLTPEEGKTHYFD-EA 328

Query: 360 GE 361
           G+
Sbjct: 329 GK 330


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: 316
Number of extensions: 10
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: 333
Length adjustment: 30
Effective length of query: 376
Effective length of database: 303
Effective search space:   113928
Effective search space used:   113928
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: 49 (23.5 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