GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcA in Pseudomonas fluorescens FW300-N2E3

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_20820 AO353_20820 sugar ABC
           transporter ATP-binding protein
          Length = 517

 Score =  131 bits (329), Expect = 3e-35
 Identities = 87/248 (35%), Positives = 130/248 (52%), Gaps = 9/248 (3%)

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

Query: 62  EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121
           +++ +G+  +  S  +A + GI  V Q L L P LS+A+N+FL          G W   +
Sbjct: 64  QMQFQGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSN----GGW---I 116

Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181
            R  + K A A ++++GL  I + +  V  L  G +Q V +AR       V+I+DEPTA 
Sbjct: 117 SRKQLRKAAIAAMAQVGLDAI-DPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAM 175

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

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



 Score = 79.7 bits (195), Expect = 1e-19
 Identities = 71/251 (28%), Positives = 118/251 (47%), Gaps = 25/251 (9%)

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

Query: 65  LEGKPIQ---FRSPMEARQAGIETVYQNL---ALSPALSIADNMFLGRE--IRKPGIMGK 116
           L G P Q    RSP +A   GI  + ++     L    SI+ N+ LG    I   GI+  
Sbjct: 316 L-GSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPVISSGGIVN- 373

Query: 117 WFRSLDRAAMEKQARAKLSELGLMTIQNIN--QAVETLSGGQRQGVAVARAAAFGSKVVI 174
              S D  A+ ++      ++  M I++ +  Q V  LSGG +Q V + R       V++
Sbjct: 374 ---SGDEMALAQR------QIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVLL 424

Query: 175 MDEPTAALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVIN 234
            DEPT  + V     +  L+ ++ R+G  +V++S ++  +  + DRI +   GR +    
Sbjct: 425 FDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFE 484

Query: 235 PKDYTMSDAVA 245
              +T  D +A
Sbjct: 485 RDSWTQDDLLA 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: 281
Number of extensions: 10
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 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