GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gguA in Pseudomonas simiae WCS417

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>lcl|FitnessBrowser__WCS417:GFF2332 PS417_11890 D-ribose transporter
           ATP-binding protein
          Length = 517

 Score =  366 bits (939), Expect = e-105
 Identities = 205/499 (41%), Positives = 314/499 (62%), Gaps = 14/499 (2%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +LE+ NI+K FPGV AL +V L+V+ G + AL+GENGAGKSTLMK+++G+Y      GEI
Sbjct: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA--GEI 80

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNE-VASNGVISWQQTFNR 123
              G    F     ++  GI +IHQEL L+P +SIAENI++G E + S  +++ ++    
Sbjct: 81  RLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRC 140

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
           T ELL ++ +   PE  + ++ + ++Q+VEIAKA+S    +LI+DEPT+++ E +   L 
Sbjct: 141 TAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLF 200

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
           +++ + ++QG   + ITHK+NEV  +AD++ V RDG  +       + ++ D +I  MVG
Sbjct: 201 SIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQ--RADSMNSDSLISMMVG 258

Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           R+L   +P R+ PIG+ +L V++            V  D++  +  GE++GIAGLMG+GR
Sbjct: 259 RELSQLFPLRETPIGDLLLTVRDLTL-------DGVFKDVSFDLHAGEILGIAGLMGSGR 311

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           T  A ++FG +     +G + +DGK V +S    AI+ G A +TEDRK  GL    ++L 
Sbjct: 312 TNVAETIFGITPSS--SGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 369

Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423
           N  +A L   +    I       +  D   +LR+++  + Q    LSGGNQQK +L++WL
Sbjct: 370 NMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 429

Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483
            +NP +LILDEPTRGIDVGAK EIY +I  LA++G  V+MISSE+PE+LG  DR+ VM+E
Sbjct: 430 MTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHE 489

Query: 484 GRIVAELPKGEASQESIMR 502
           G ++  L + EA+QE +M+
Sbjct: 490 GELMGTLDRSEATQEKVMQ 508


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: 47
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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