GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Marinobacter adhaerens HP15

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= uniprot:D8IPI1
         (406 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  291 bits (745), Expect = 2e-83
 Identities = 155/370 (41%), Positives = 233/370 (62%), Gaps = 6/370 (1%)

Query: 1   MADIHCQALAKHYAG-GPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59
           M+ +  +++ K Y G     L  +D+ I  GEF++L+GPSGCGKST++  IAGLE I+ G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 60  TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119
           ++ + G  ++ +  ++R++AMVFQ+YALYP MSV +NIAFGL+    P  EID+ V  VA
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 120 ALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKR 179
            LL +  L+ +KP  +SGGQQQR A+ RA+ + P ++LFDEPLSNLDAKLR ++R +IK+
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 180 LHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPA 239
           LHQRL+TT VYVTHDQ+EAMTLADR+ +++DG + Q G+P E+Y  P NLF AGF+G+PA
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 240 MNFLSGTVQRQDGQLFIETA---HQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREP 296
           M+F+  TV++ +G L  E      +   L    F   R    V L +RP+H+    +++ 
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300

Query: 297 AASLTC--PVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHV 354
             +L      ++E+ E  G D +   +  D  +   +  +     G T  L  D  ++  
Sbjct: 301 DQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKVVF 360

Query: 355 FDVESGENLS 364
           FD E+ + ++
Sbjct: 361 FDPETEKRIA 370


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: 407
Number of extensions: 15
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: 372
Length adjustment: 30
Effective length of query: 376
Effective length of database: 342
Effective search space:   128592
Effective search space used:   128592
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