GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pantoea rwandensis LMG 26275

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_084931762.1 HA51_RS02835 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>NCBI__GCF_002095475.1:WP_084931762.1
          Length = 500

 Score =  164 bits (415), Expect = 3e-45
 Identities = 95/248 (38%), Positives = 146/248 (58%), Gaps = 13/248 (5%)

Query: 7   LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66
           L  RG+ K YG   AL   DF + PGE+ A+IG+NGAGKS+++  +SG    D G I + 
Sbjct: 6   LMMRGITKTYGSAIALQDVDFMVRPGEVHALIGENGAGKSTLLNILSGVRPADSGAIHVN 65

Query: 67  GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126
           G+ +Q ++P+ AR AGI  ++Q L   P LS+A NMFLGR +           +L+   +
Sbjct: 66  GEQVQMKNPLSARHAGIAMIHQELQHVPELSVAQNMFLGRPL----------TTLNGLFV 115

Query: 127 EKQAR-AKLSELGLMTIQNINQA--VETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALG 183
           +K+A+ A+ + +      +IN A  ++ L   Q+Q V +ARA    +K++ MDEPT++L 
Sbjct: 116 DKRAQLARATHILKQLDPSINPAEPIKNLKVSQQQIVEIARALLDEAKIIAMDEPTSSLT 175

Query: 184 VKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDA 243
            +E  R+ ELI D++  G+ ++ +SH M  +F+V DR  I R GR++ V+N  D T    
Sbjct: 176 PREFERLAELIADLKSTGVSLIYVSHKMNEIFQVCDRATIMRDGRQVGVVNICDETEETI 235

Query: 244 VAFMTGAK 251
           VA M G K
Sbjct: 236 VAKMVGRK 243



 Score = 93.6 bits (231), Expect = 7e-24
 Identities = 69/239 (28%), Positives = 116/239 (48%), Gaps = 13/239 (5%)

Query: 13  VKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQF 72
           V+   R T +  A F +  GE+L V G  GAG++ ++K I+G      GE+R+ G+ ++ 
Sbjct: 261 VENVARGTEIKPASFSVCAGEVLGVAGLVGAGRTELLKLIAGIDKRSAGEVRVNGQLVRN 320

Query: 73  RSPMEARQAGIETVYQNL---ALSPALSIADNMFLG--REIRKPGIMGKWFRSLDRAAME 127
            +   A +AGI  V ++     +  A ++  NM L   R     G++ K    L+  A E
Sbjct: 321 HNVSAAIRAGIGLVPEDRKKEGIIKARAVKVNMALPSMRNFTLAGVIRKV--KLNAVAQE 378

Query: 128 KQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKES 187
             +  KL  L      NI + + TLSGG +Q V + R  A  ++V + DEPT  + +   
Sbjct: 379 VMSDLKLRPL------NIEKPIGTLSGGNQQKVIIGRWVAADAEVFLFDEPTRGIDIGAK 432

Query: 188 RRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAF 246
             +  LI  + ++G  IV++S  M  +  V+DR+ + R G+    +   D T  +   F
Sbjct: 433 AEIYNLIEKLAQQGKAIVVVSSEMTEILRVSDRVLVMREGKITRELTGDDITEENIARF 491


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: 283
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: 500
Length adjustment: 29
Effective length of query: 231
Effective length of database: 471
Effective search space:   108801
Effective search space used:   108801
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 24 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