Aligments for a candidate for xylG in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Aligments for a candidate for xylG in Pseudomonas fluorescens FW300-N2E2

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008
          Length = 485

 Score =  367 bits (943), Expect = e-106
 Identities = 208/476 (43%), Positives = 314/476 (65%), Gaps = 18/476 (3%)

Query: 35  IVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRG-VRWNH--PSEAINAGIVTVFQELSVM 91
           ++GENGAGKST++KI+AG    D G+   E  G V   H  P      GI+T++QE +++
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60

Query: 92  DNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVE 151
            ++SVAEN+++G E  R  F+D+K+M+ +A+  + ++ G+ I P   + K S+A QQMVE
Sbjct: 61  ADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVL-DDLGLHITPRTMVRKLSVAEQQMVE 119

Query: 152 IARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKV 211
           IA+A+   AK++I+DEPT++L+ +E +KL E++  LK KG++II++SH+L E+   CD+ 
Sbjct: 120 IAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRY 179

Query: 212 SVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEKFYIKEAHEPGEVVLEVKNLS-----GE 266
           ++ RDG YI +  + +++ + IV +MVGR +E         PGEV+L+V+++S     G 
Sbjct: 180 TIFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAAGGG 239

Query: 267 R------FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVE-IN 319
           R        ++S  +R GEI+GFAGLVGAGRTEL   IFG      G IY+ G++V    
Sbjct: 240 RSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPFK 299

Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK-GPFISFKREKELADWAI 378
            P + I  G+ LVPEDRK+    L  SI  N+SLPSL  +++ G FI  + E +L     
Sbjct: 300 SPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDYQ 359

Query: 379 KTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMS 438
           K   I+ +     +  LSGGNQQKV+LA+ +ALKPK+LI+DEPTRGIDVGAKAE+++++ 
Sbjct: 360 KRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQLLF 419

Query: 439 QLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVM-KLAAGL 493
            +A+ GV VI+ISSELPEV+ +SDRI     G++ GI+ A EA++E +M ++A G+
Sbjct: 420 DMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMAQGV 475



 Score = 91.7 bits (226), Expect = 5e-23
 Identities = 72/250 (28%), Positives = 122/250 (48%), Gaps = 19/250 (7%)

Query: 4   ILEVKSIHKRFPG----VHA--LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPD 57
           +L+V+S+ +   G    +HA  L  +S++   GE+    G  GAG++ L ++I G    D
Sbjct: 225 MLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCD 284

Query: 58  EGEIIYEGRGVR-WNHPSEAINAGIVTV---------FQELSVMDNLSVAENIFMGDEEK 107
           EG I   GR V  +  P E I AG+  V         F   S+  N+S+     +G  ++
Sbjct: 285 EGMIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPS---LGGLQR 341

Query: 108 RGIFIDYKKMYREAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDE 167
            G+FID +   +  + + K       +    +G  S   QQ V +AR +  K KVLI+DE
Sbjct: 342 WGMFIDDRAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDE 401

Query: 168 PTSSLTQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIEN 227
           PT  +      ++ +++  +   GVA+I IS  L E+  + D++   R+G+  G  S + 
Sbjct: 402 PTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADE 461

Query: 228 LTKEKIVEMM 237
            T+E ++  M
Sbjct: 462 ATEELLMARM 471


Lambda     K      H
   0.318    0.138    0.385 

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: 620
Number of extensions: 26
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: 494
Length of database: 485
Length adjustment: 34
Effective length of query: 460
Effective length of database: 451
Effective search space:   207460
Effective search space used:   207460
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 (21.7 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:

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, 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

GapMind for catabolism of small carbon sources