GapMind for catabolism of small carbon sources

 

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

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034
          Length = 517

 Score =  311 bits (797), Expect = 4e-89
 Identities = 186/509 (36%), Positives = 290/509 (56%), Gaps = 13/509 (2%)

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

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

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

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

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

Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361
           GRTE    +FG       T  +    + V + +   A+  G+A +TEDRK  GL+L  +I
Sbjct: 295 GRTELLRLIFGADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSI 354

Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421
             N  L N+  +S    +++  EM +A      +RIRSS   Q    LSGGNQQKVV+ +
Sbjct: 355 SANIALGNMPVISSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGR 414

Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481
           WL  +  V++ DEPTRGIDVGAK++IY ++ +L   GK ++++SS++ EL+  CDRI V+
Sbjct: 415 WLERDCTVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVL 474

Query: 482 NEGRIVAELPKGEASQESIMRAIMRSGEK 510
           + GR++    +   +Q+ ++ A     +K
Sbjct: 475 SAGRLIDTFERDSWTQDDLLAAAFAGYQK 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: 594
Number of extensions: 29
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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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