GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Pseudomonas fluorescens FW300-N2C3

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  363 bits (932), Expect = e-105
 Identities = 202/499 (40%), Positives = 312/499 (62%), Gaps = 14/499 (2%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +LE+ N++K FPGV AL +V L+V+ G + AL+GENGAGKSTLMK+++G+Y      GE+
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA--GEL 83

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123
              G    F     +   GI +IHQEL L+P +SIAENI++G E  +   ++   +    
Sbjct: 84  RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRC 143

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
           T  LL+++ +K  PE  + ++ + ++Q+VEIAKA+S    +LI+DEPT+++ E++   L 
Sbjct: 144 TARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLF 203

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
           +++ + ++QG   I ITHK+NEV  +AD++ V RDG  +       + +  D +I  MVG
Sbjct: 204 SIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQ--RADSMDGDSLISMMVG 261

Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           R+L   +P R+ PIGE +L V++ +          +   ++  +  GE++GIAGLMG+GR
Sbjct: 262 RELSQLFPVREQPIGELVLSVRDLSL-------DGIFKGVSFDLHAGEILGIAGLMGSGR 314

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           T  A ++FG +      G++ +DG+PV +S    AI+ G A +TEDRK  GL    ++L 
Sbjct: 315 TNVAEAIFGVTPS--TGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 372

Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423
           N  +A L        I       +  D   +LR+++  + Q    LSGGNQQK +L++WL
Sbjct: 373 NMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 432

Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483
            +NP +LILDEPTRGIDVGAK EIY +I+ LA++G  V+MISSE+PE+LG  DR+ VM+E
Sbjct: 433 MTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHE 492

Query: 484 GRIVAELPKGEASQESIMR 502
           G ++  L + EA+QE +M+
Sbjct: 493 GDLMGTLDRSEATQERVMQ 511


Lambda     K      H
   0.316    0.135    0.374 

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: 602
Number of extensions: 37
Number of successful extensions: 10
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: 512
Length of database: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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