GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas simiae WCS417

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__WCS417:GFF2673
          Length = 510

 Score =  153 bits (386), Expect = 8e-42
 Identities = 92/250 (36%), Positives = 141/250 (56%), Gaps = 10/250 (4%)

Query: 1   MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60
           M+ EP+L  +G+ K +  +  L      +YPGEI A++G+NGAGKS+++K +SGA   D 
Sbjct: 1   MSLEPLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADP 60

Query: 61  G-EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFR 119
           G EIR+ G+ I    P  A+  GI  +YQ L+L P LS+A+N++LGRE+R+      W  
Sbjct: 61  GGEIRIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRG-----W-- 113

Query: 120 SLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179
           ++DR  ME      L  LG          V +LS  +RQ V +ARA    +K+++MDEPT
Sbjct: 114 TIDRKGMEAGCIEVLQRLGAEFTPATR--VSSLSIAERQLVEIARALHAHAKILVMDEPT 171

Query: 180 AALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYT 239
             L  +E+ R+  LI  +R +GL I+ ISH M  ++ ++DR+ + R G  +  +     +
Sbjct: 172 TPLSSRETDRLFALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALS 231

Query: 240 MSDAVAFMTG 249
               V  M G
Sbjct: 232 AEALVKMMVG 241



 Score = 76.3 bits (186), Expect = 1e-18
 Identities = 57/206 (27%), Positives = 100/206 (48%), Gaps = 9/206 (4%)

Query: 27  FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ-FRSPMEARQAGIET 85
           FDL+ GE+L + G  GAG++ + + I  A     G + + GK +   R+P +A +AG+  
Sbjct: 278 FDLHAGEVLGIAGLVGAGRTELARLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVY 337

Query: 86  VYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTI 142
           + ++     L   +S+ADN+ +   +      G     LDR    +++   +  L +   
Sbjct: 338 LTEDRKAQGLFLDMSVADNINVCACVPDAHAGGV----LDRDHALQRSNDAIKSLSIRVA 393

Query: 143 QNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGL 202
                A   LSGG +Q V +AR       V+I+DEPT  + +     +  +I  + + G+
Sbjct: 394 SGKVNA-GALSGGNQQKVLLARLLEVKPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGI 452

Query: 203 PIVLISHNMPHVFEVADRIHIHRLGR 228
            IV+IS  +P +    DR+ I R G+
Sbjct: 453 GIVVISSELPEIIGTCDRVLIMREGQ 478


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: 284
Number of extensions: 18
Number of successful extensions: 5
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: 510
Length adjustment: 29
Effective length of query: 231
Effective length of database: 481
Effective search space:   111111
Effective search space used:   111111
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