GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pseudomonas fluorescens FW300-N1B4

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034
          Length = 517

 Score =  130 bits (327), Expect = 6e-35
 Identities = 86/248 (34%), Positives = 128/248 (51%), Gaps = 9/248 (3%)

Query: 2   AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61
           A   +L+  G+ K Y +   L   D  L  GE+LA+ G+NGAGKS++ K I G V P  G
Sbjct: 5   APNAVLSVSGIGKTYAQ-PVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTG 63

Query: 62  EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121
           ++R +G+  +  S  +A + GI  V Q L L P LS+A+N+FL       G + +  + L
Sbjct: 64  QMRFQGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHGGWISR--KQL 121

Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181
            +AA+E  A+  L  +   T+      V  L  G +Q V +AR       V+I+DEPTA 
Sbjct: 122 RKAAIEAMAQVGLDAIDPDTL------VGELGIGHQQMVEIARNLIGDCHVLILDEPTAM 175

Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241
           L  +E   + E I  ++ RG+ I+ ISH +  +  VA RI + R G  +CV    +Y   
Sbjct: 176 LTAREVEMLFEQITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSE 235

Query: 242 DAVAFMTG 249
             V  M G
Sbjct: 236 QLVTLMVG 243



 Score = 79.7 bits (195), Expect = 1e-19
 Identities = 67/249 (26%), Positives = 118/249 (47%), Gaps = 21/249 (8%)

Query: 5   PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64
           P LT +GL     R   +    F++  GEI  + G  GAG++ +++ I GA T D G + 
Sbjct: 260 PALTVKGLT----RSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADTADSGTVA 315

Query: 65  L--EGKPIQFRSPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIM-GKWF 118
           L    + +  RSP +A   GI  + ++     L    SI+ N+ LG     P I  G + 
Sbjct: 316 LGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGN---MPVISSGGFV 372

Query: 119 RSLDRAAMEKQARAKLSELGLMTIQNIN--QAVETLSGGQRQGVAVARAAAFGSKVVIMD 176
            + D  ++ ++      ++  M I++ +  Q V  LSGG +Q V + R       V++ D
Sbjct: 373 NNGDEMSLAQR------QINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVMLFD 426

Query: 177 EPTAALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPK 236
           EPT  + V     +  L+ ++ R+G  +V++S ++  +  + DRI +   GR +      
Sbjct: 427 EPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERD 486

Query: 237 DYTMSDAVA 245
            +T  D +A
Sbjct: 487 SWTQDDLLA 495


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: 267
Number of extensions: 9
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: 517
Length adjustment: 30
Effective length of query: 230
Effective length of database: 487
Effective search space:   112010
Effective search space used:   112010
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