GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA 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:

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