GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Klebsiella michiganensis M5al

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__Koxy:BWI76_RS03270
          Length = 376

 Score =  308 bits (789), Expect = 2e-88
 Identities = 168/379 (44%), Positives = 233/379 (61%), Gaps = 22/379 (5%)

Query: 1   MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           MA +  + + K Y  G   +H +DL I DGEF+V +GPSGC KST LRMIAGLEDISGG 
Sbjct: 1   MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60

Query: 61  LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120
           + IG   VNDLP ++R +AMVFQNYALYPH +V+DN+AFGL+  KRP  EI RRV + A 
Sbjct: 61  IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120

Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180
            L +  LL RKP+ MSGGQ+QR A+ RAI++ P VFLFDEPLSNLDAKLR  +R  I +L
Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180

Query: 181 HQRLR-----TTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFI 235
           H+ L+      T +YVTHDQ EA+TL DR+ ++  G I+Q  +P +LY YP N F A FI
Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240

Query: 236 GTPAMNFLSGTVQRQDGQLFIETA--------HQRWALTGERFSRLRHAMAVKLAVRPDH 287
           G+P++N +   +++ + +L++E A        H +  L     ++      V   +RP+H
Sbjct: 241 GSPSINLIDTAIRKNNERLYVEIAPGVEILIPHSKQVLLEGYINK-----PVCFGIRPEH 295

Query: 288 VRIAGEREPAASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLP--QPGATLTL 345
           + +A + +   +    ++V  VE +G++  L    G + L A V    +     G TL  
Sbjct: 296 ISLASDDDDLNTFEGVLTV--VENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLRF 353

Query: 346 ALDQHELHVFDVESGENLS 364
            L+    HVFD  +  NL+
Sbjct: 354 NLNTAFCHVFDFYNENNLT 372


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: 370
Number of extensions: 11
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: 376
Length adjustment: 31
Effective length of query: 375
Effective length of database: 345
Effective search space:   129375
Effective search space used:   129375
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