GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_993 Ribose ABC transport
           system, ATP-binding protein RbsA (TC 3.A.1.2.1)
          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 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