GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gguA in Pseudomonas fluorescens FW300-N2E3

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21385 AO353_21385 D-ribose
           transporter ATP-binding protein
          Length = 521

 Score =  361 bits (926), Expect = e-104
 Identities = 201/499 (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: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA--GEL 84

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123
              G    F     +   GI +IHQEL L+P +SIAENI++G E  +   +I  ++    
Sbjct: 85  RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRC 144

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
           T +LL+++ +   PE  + ++ + ++Q+VEIAKA+S    +LI+DEPT+++ + +   L 
Sbjct: 145 TAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLF 204

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
           +++ + + QG   I ITHK+NEV  +AD++ V RDG  +       + +  D +I  MVG
Sbjct: 205 SIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQ--RADSMDGDSLISMMVG 262

Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           R+L   +P R+ PIG+ ++ V++        R   V   ++  +  GE++GIAGLMG+GR
Sbjct: 263 RELSQLFPVREKPIGDLLMSVRDL-------RLDGVFKGVSFDLHAGEILGIAGLMGSGR 315

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           T  A ++FG +      G++ +DG+PV +S    AI+ G A +TEDRK  GL    ++L 
Sbjct: 316 TNVAEAIFGITPSDG--GEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 373

Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423
           N  +A L   +    I       +  D   +LR+++  + Q    LSGGNQQK +L++WL
Sbjct: 374 NMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 433

Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483
            +NP +LILDEPTRGIDVGAK EIY +I+ LA++G  V+MISSE+PE+LG  DR+ VM+E
Sbjct: 434 MTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHE 493

Query: 484 GRIVAELPKGEASQESIMR 502
           G ++  L + EA+QE +M+
Sbjct: 494 GDLMGTLDRSEATQERVMQ 512


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: 619
Number of extensions: 41
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: 521
Length adjustment: 35
Effective length of query: 477
Effective length of database: 486
Effective search space:   231822
Effective search space used:   231822
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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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