GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas fluorescens FW300-N2E2

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Pf6N2E2_993 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_993
          Length = 501

 Score =  146 bits (368), Expect = 1e-39
 Identities = 90/260 (34%), Positives = 137/260 (52%), Gaps = 11/260 (4%)

Query: 1   MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60
           M  + I+   GL K YG +TAL   DF+L  GEI  + G+NGAGKS+++K + G V P E
Sbjct: 1   MQSQKIVQVTGLHKTYGGITALKSIDFELNAGEIHGLCGENGAGKSTLVKILGGLVQPTE 60

Query: 61  GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRS 120
           G+I  +G  +  R       + I  V+Q L++ PALS+ DN+ +G        +G+ +  
Sbjct: 61  GQILFDGAVL--RPGRRTDPSCISIVHQELSIIPALSVLDNVLMGN-----AQVGRLYL- 112

Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180
             R   +   R +L  +GL  +  ++Q+   LS  +RQ V ++R    G+KV+I+DEPTA
Sbjct: 113 --RGRFKNDVRRQLDSIGLSHV-TLDQSASELSLAERQLVEISRCVLHGAKVLILDEPTA 169

Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTM 240
            L   E  RV   +  +R +G  +V ISH +  VF++ DRI I R G R+      + T 
Sbjct: 170 TLAESEIARVFTAVRWLRDQGTTVVFISHRLNEVFDLTDRITIFRSGERVLTAPTSEMTT 229

Query: 241 SDAVAFMTGAKEPPREAIAA 260
              V  M G +   R  + A
Sbjct: 230 ESLVLAMVGHEVERRSTLDA 249



 Score = 88.6 bits (218), Expect = 2e-22
 Identities = 61/212 (28%), Positives = 103/212 (48%), Gaps = 14/212 (6%)

Query: 15  RYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRS 74
           R+G   A    D ++  GEIL V+G  G+G   +I+AI+G V    G + ++G+ +  +S
Sbjct: 263 RFGVPNACQSLDLEVPAGEILGVVGQLGSGADRLIEAIAG-VRSHTGNLSIDGQQVDIQS 321

Query: 75  PMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFR-----SLDRAAMEKQ 129
           P +A       + Q +A  P       +FL   I +       F+      L+R + E+ 
Sbjct: 322 PRKA-------ISQGIAYVPEDRAGKGVFLEANIGQNSTASILFQFSRFGRLER-SQERD 373

Query: 130 ARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRR 189
           A   L +   +    I   V +LSGG +Q VA+A+AAA   K++I++EPT  + V     
Sbjct: 374 AALDLMKRFTIDTTRIGSKVSSLSGGNQQKVAMAKAAAISPKILILNEPTRGVDVGARAE 433

Query: 190 VLELILDVRRRGLPIVLISHNMPHVFEVADRI 221
           +   +  +   GL ++  S +   V E+ADR+
Sbjct: 434 IYAQLRSMAATGLTVIFFSTDFEEVLELADRV 465


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: 280
Number of extensions: 16
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: 501
Length adjustment: 29
Effective length of query: 231
Effective length of database: 472
Effective search space:   109032
Effective search space used:   109032
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