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_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121
          Length = 514

 Score =  311 bits (798), Expect = 3e-89
 Identities = 179/498 (35%), Positives = 293/498 (58%), Gaps = 13/498 (2%)

Query: 6   LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65
           L    I KTFPGVKAL+N++     G++HAL+GENGAGKSTL+K+L G Y   +  G + 
Sbjct: 16  LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCS--GALQ 73

Query: 66  YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125
                 +F++  DS   G+ +IHQEL LVP +++AEN+FLG+  AS G+I+      +  
Sbjct: 74  IGERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQAL 133

Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185
             LK +  +  P+  +  + +G++QLVEIAKALS+   ++  DEPT+SL+  + + L+ +
Sbjct: 134 ACLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAI 193

Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGRD 245
           +   R++G   + ++H++ EV ++ + +TV +DG  V+T D    +++ D ++  MVGRD
Sbjct: 194 IGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFD-DMSQLTHDQLVTCMVGRD 252

Query: 246 LEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTE 305
           ++D Y  R    G   L+V              +   ++  V KGE++G+ GL+GAGRTE
Sbjct: 253 IQDIYDYRPRQRGAVALKVDGL-------LGPGLREPVSFEVHKGEILGLFGLVGAGRTE 305

Query: 306 FAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNT 365
               + G        G + + G  + + + R AI AG+    EDRK  G++   ++  N 
Sbjct: 306 LLRLLSG--LARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENI 363

Query: 366 TL-ANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424
            + A  A  +   ++  + E   A      L++++    Q+ + LSGGNQQK +L +WL 
Sbjct: 364 NISARGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLS 423

Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484
               VL+LDEPTRGID+GAK EIY II+ LAA+G  V+++SS++ E++G  DRI V+ EG
Sbjct: 424 MPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEG 483

Query: 485 RIVAELPKGEASQESIMR 502
            +  EL + +A++ ++++
Sbjct: 484 ALRGELSREQANESNLLQ 501


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: 589
Number of extensions: 23
Number of successful extensions: 9
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: 514
Length adjustment: 35
Effective length of query: 477
Effective length of database: 479
Effective search space:   228483
Effective search space used:   228483
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