Alignments for a candidate for gguA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Pseudomonas fluorescens FW300-N2E2

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008
          Length = 485

 Score =  324 bits (830), Expect = 5e-93
 Identities = 192/484 (39%), Positives = 298/484 (61%), Gaps = 13/484 (2%)

Query: 36  LVGENGAGKSTLMKVLSGVYPAGTYEGEIHYEGAVRNFRAIN-DSEDIGIIIIHQELALV 94
           L+GENGAGKST++K+L+G  PA   +G + + G V          +++GII I+QE  L+
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60

Query: 95  PLLSIAENIFLGNEVASNGVISWQQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEI 154
             +S+AEN++LG E   +G + W+Q F+  + +L  +GL  +P T++  + V +QQ+VEI
Sbjct: 61  ADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVEI 120

Query: 155 AKALSKSVKLLILDEPTASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQIT 214
           AKAL+ + KL+I+DEPTA+L+  + + L  ++ + + +G++ I ++HKLNEV+   D+ T
Sbjct: 121 AKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRYT 180

Query: 215 VLRDGMTVKTLD-CHQEEISEDVIIRNMVGRDLEDRYPPRDVPIGETILEVKNWN---AY 270
           + RDG  + + D C   ++S D I+R MVGRD+E    P     GE +L+V++ +   A 
Sbjct: 181 IFRDGAYITSGDVC---DVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAAG 237

Query: 271 HQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPV 330
             +      L D++V VR GE+VG AGL+GAGRTE A  +FG        G + ++G+ V
Sbjct: 238 GGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDE--GMIYVNGRQV 295

Query: 331 D-VSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSK-ASIIDDIKEMKVA 388
               + R+ I AG+A V EDRK     L+ +I  N +L +L G+ +    IDD  E ++ 
Sbjct: 296 SPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLI 355

Query: 389 SDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIY 448
            D++ RLRI+ S        LSGGNQQKV+L++ +   P VLI+DEPTRGIDVGAK E++
Sbjct: 356 QDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVH 415

Query: 449 TIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSG 508
            ++  +A  G  V++ISSE+PE++   DRI    EG+I   +   EA++E +M A M  G
Sbjct: 416 QLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLM-ARMAQG 474

Query: 509 EKNS 512
             +S
Sbjct: 475 VSSS 478



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 65/258 (25%), Positives = 123/258 (47%), Gaps = 32/258 (12%)

Query: 5   ILEMRNITKTFPG------VKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAG 58
           +L+++++++T  G         L ++++ V+ GEI    G  GAG++ L +V+ G    G
Sbjct: 225 MLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGA--DG 282

Query: 59  TYEGEIHYEG-AVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN----- 112
             EG I+  G  V  F++  +    G+       ALVP     +  FL + +  N     
Sbjct: 283 CDEGMIYVNGRQVSPFKSPREGIAAGV-------ALVPEDRKQQACFLSHSIRWNMSLPS 335

Query: 113 --GVISWQQTFNRTRE------LLKKVGLKESPETL-ITDIGVGKQQLVEIAKALSKSVK 163
             G+  W    +   E        K++ +K S +++ I  +  G QQ V +A+ ++   K
Sbjct: 336 LGGLQRWGMFIDDRAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPK 395

Query: 164 LLILDEPTASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVK 223
           +LI+DEPT  ++      +  LL +    G+  I+I+ +L EV  V+D+I   R+G    
Sbjct: 396 VLIVDEPTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITG 455

Query: 224 TLDCHQEEISEDVIIRNM 241
            +    +E +E++++  M
Sbjct: 456 IVSA--DEATEELLMARM 471


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: 583
Number of extensions: 35
Number of successful extensions: 9
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: 512
Length of database: 485
Length adjustment: 34
Effective length of query: 478
Effective length of database: 451
Effective search space:   215578
Effective search space used:   215578
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)
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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