GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas fluorescens FW300-N2E3

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21385
          Length = 521

 Score =  147 bits (372), Expect = 3e-40
 Identities = 83/236 (35%), Positives = 132/236 (55%), Gaps = 8/236 (3%)

Query: 14  KRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFR 73
           K +  V AL      + PG +LA++G+NGAGKS+++K I+G   PD GE+RL GKP+ F 
Sbjct: 35  KGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFD 94

Query: 74  SPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAK 133
           +P+ A QAGI  ++Q L L P +SIA+N+++GRE          F  +D   M +     
Sbjct: 95  TPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE------QLNGFHMIDHREMHRCTAQL 148

Query: 134 LSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLEL 193
           L  L +    +  + V  LS  +RQ V +A+A ++ S ++IMDEPT+A+  KE   +  +
Sbjct: 149 LERLRINL--DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206

Query: 194 ILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249
           I D++ +G  I+ I+H M  VF +AD + + R G  + +           ++ M G
Sbjct: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVG 262



 Score =  100 bits (250), Expect = 5e-26
 Identities = 63/226 (27%), Positives = 115/226 (50%), Gaps = 9/226 (3%)

Query: 27  FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETV 86
           FDL+ GEIL + G  G+G++++ +AI G    D GEI L+G+P++   P  A + G   +
Sbjct: 297 FDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALL 356

Query: 87  YQNLALS---PALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQ 143
            ++  LS   P LS+ +NM +      P   G  F  + + A+         +L + T  
Sbjct: 357 TEDRKLSGLFPCLSVLENMEMAV---LPHYAGNGF--IQQKALRALCEDMCKKLRVKT-P 410

Query: 144 NINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLP 203
           ++ Q ++TLSGG +Q   +AR      +++I+DEPT  + V     +  LI  +   G+ 
Sbjct: 411 SLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMA 470

Query: 204 IVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249
           +++IS  +P V  ++DR+ +   G  +  ++  + T    +   +G
Sbjct: 471 VIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 516


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: 288
Number of extensions: 14
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: 521
Length adjustment: 30
Effective length of query: 230
Effective length of database: 491
Effective search space:   112930
Effective search space used:   112930
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