GapMind for catabolism of small carbon sources

 

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

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  144 bits (362), Expect = 5e-39
 Identities = 82/244 (33%), Positives = 133/244 (54%), Gaps = 8/244 (3%)

Query: 6   ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65
           +L    + K +  V AL      + PG +LA++G+NGAGKS+++K I+G   PD GE+RL
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85

Query: 66  EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125
            GKP+ F +P+ A QAGI  ++Q L L P +SIA+N+++GRE             +D   
Sbjct: 86  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE------QLNGLHMVDHGE 139

Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185
           M +     L  L +    +  + V  LS  +RQ V +A+A ++ S ++IMDEPT+A+   
Sbjct: 140 MHRCTARLLERLRIKL--DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITET 197

Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVA 245
           E   +  +I D++ +G  I+ I+H M  VF +AD + + R G  + +           ++
Sbjct: 198 EVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLIS 257

Query: 246 FMTG 249
            M G
Sbjct: 258 MMVG 261



 Score =  102 bits (254), Expect = 2e-26
 Identities = 63/226 (27%), Positives = 116/226 (51%), Gaps = 9/226 (3%)

Query: 27  FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETV 86
           FDL+ GEIL + G  G+G++++ +AI G      GEIRL+G+P++   P  A + G   +
Sbjct: 296 FDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALL 355

Query: 87  YQNLALS---PALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQ 143
            ++  LS   P LS+ +NM +      P  +G  F  + + A+         +L + T  
Sbjct: 356 TEDRKLSGLFPCLSVLENMEMAV---LPHYVGNGF--IQQKALRALCEDMCKKLRVKT-P 409

Query: 144 NINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLP 203
           ++ Q ++TLSGG +Q   +AR      +++I+DEPT  + V     +  LI  +   G+ 
Sbjct: 410 SLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMA 469

Query: 204 IVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249
           +++IS  +P V  ++DR+ +   G  +  ++  + T    +   +G
Sbjct: 470 VIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 515


Lambda     K      H
   0.321    0.136    0.383 

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: 292
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 517
Length adjustment: 30
Effective length of query: 230
Effective length of database: 487
Effective search space:   112010
Effective search space used:   112010
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: 49 (23.5 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