Alignments for a candidate for gguA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Pseudomonas fluorescens GW456-L13

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911
          Length = 517

 Score =  320 bits (821), Expect = 6e-92
 Identities = 195/512 (38%), Positives = 295/512 (57%), Gaps = 19/512 (3%)

Query: 3   NTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEG 62
           N +L +  I KT+     L  ++L +  GE+ AL GENGAGKSTL K++ G+    T  G
Sbjct: 7   NAVLSVSGIGKTY-AQPVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTT--G 63

Query: 63  EIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFN 122
           ++ Y+G      +   +E +GI ++ QEL L+P LS+AEN+FL N  +  G IS +Q   
Sbjct: 64  QMQYQGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQLRK 123

Query: 123 RTRELLKKVGLKE-SPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181
              E +  VGL    P+TL+ ++G+G QQ+VEIA+ L     +LILDEPTA L   + E 
Sbjct: 124 AAIEAMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEM 183

Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNM 241
           L   +   +++G++ I I+H+L E+ +VA +I VLRDG  V          + + ++  M
Sbjct: 184 LFEQITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEP--MANYNSEQLVTLM 241

Query: 242 VGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGA 301
           VGR+L +        IG  +L V   +   +       + D++  VR GE+ GI+GL+GA
Sbjct: 242 VGRELGEHIDMGARKIGAPVLTVNGLSRSDK-------VRDVSFEVRAGEIFGISGLIGA 294

Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDA---GLAYVTEDRKHLGLVLN 358
           GRTE    +FG       +G + + G P  V  VR  +DA   G+A +TEDRK  GL+L 
Sbjct: 295 GRTELLRLIFGADIAD--SGTIAL-GAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLT 351

Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418
            +I  N  L N+ G+S A  +D+ KE  +A      +RIRSSG  Q    LSGGNQQKVV
Sbjct: 352 QSIGANIALGNMPGISGAGFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVV 411

Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478
           + +WL  +  VL+ DEPTRGIDVGAK++IY ++ +L   GK ++++SS++ EL+  CDRI
Sbjct: 412 IGRWLERDCSVLLFDEPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRI 471

Query: 479 YVMNEGRIVAELPKGEASQESIMRAIMRSGEK 510
            V++ G ++    +   +Q+ ++ A     +K
Sbjct: 472 GVLSAGSLIDTFDRDSWTQDELLAAAFAGYQK 503


Lambda     K      H
   0.316    0.135    0.374 

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: 598
Number of extensions: 33
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 512
Length of database: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources