GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas putida KT2440

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Putida:PP_2455
          Length = 524

 Score =  119 bits (299), Expect = 1e-31
 Identities = 84/249 (33%), Positives = 126/249 (50%), Gaps = 9/249 (3%)

Query: 1   MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60
           +A E +L A GL K Y +   L      L  GE+LA+ G+NGAGKS++ K ISG   P  
Sbjct: 11  LANEVVLAASGLGKTYAQ-PVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTT 69

Query: 61  GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRS 120
           G +   G+     S  EA + G+  V Q L L P L++A+N+FL         +   F  
Sbjct: 70  GHMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDN-------LPSRFGW 122

Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180
           +    + + A A ++ +GL  I + +  V  L  G +Q V +AR       V+I+DEPTA
Sbjct: 123 ISHKRLRQLATAAMARVGLDAI-DPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTA 181

Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTM 240
            L  +E   +   I  +R RG+ IV ISH +  +  VA RI + R G+ +C    + Y+ 
Sbjct: 182 MLTAREVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSS 241

Query: 241 SDAVAFMTG 249
           ++ V  M G
Sbjct: 242 AELVNLMVG 250



 Score = 76.3 bits (186), Expect = 1e-18
 Identities = 65/241 (26%), Positives = 115/241 (47%), Gaps = 20/241 (8%)

Query: 27  FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKP--IQFRSPMEARQAGIE 84
           F++  GEI  + G  GAG++ +++ I GA   D G I L   P  +   SP  A +AGI 
Sbjct: 285 FEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIA 344

Query: 85  TVYQNL---ALSPALSIADNMFLGR--EIRKPGIMGKWFRSLDRAAMEKQARAKLSELGL 139
            + ++     L    SI+ N+ LG    + + G++       ++A  E+Q +A       
Sbjct: 345 LITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDS---EAEKALAERQIQA------- 394

Query: 140 MTIQNIN--QAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDV 197
           M I++    Q V  LSGG +Q V + R      +V++ DEPT  + V     +  L+ ++
Sbjct: 395 MRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAEL 454

Query: 198 RRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGAKEPPREA 257
            R+G  +V++S ++  +  + DRI +   GR +     +D+   D +     A    R+A
Sbjct: 455 ARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTF-ARDHWSQDQLLAAAFAGYQKRDA 513

Query: 258 I 258
           +
Sbjct: 514 L 514


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: 289
Number of extensions: 11
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: 524
Length adjustment: 30
Effective length of query: 230
Effective length of database: 494
Effective search space:   113620
Effective search space used:   113620
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