GapMind for catabolism of small carbon sources

 

Alignments 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_5969 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969
          Length = 514

 Score =  385 bits (990), Expect = e-111
 Identities = 201/491 (40%), Positives = 321/491 (65%), Gaps = 8/491 (1%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           L    I K FPGV AL  +S   +PG+VHA++GENGAGKSTL+KI+ G Y P  G++   
Sbjct: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124
            + + +   +++I +G+  + QEL ++  ++VAEN+F+G    R   ++   + ++A   
Sbjct: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTL 135

Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184
           +K     EIDP+EK+G+ S+  +Q+VEIA+A+ + A V+  DEPTSSL+ +E ++L  ++
Sbjct: 136 LKG-LADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194

Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGT-DSIENLTKEKIVEMMVGRKLE 243
             L+++G  ++++SHR+EE+F IC+ V+V +DG Y+ T +++  LT +++V  MVGR ++
Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254

Query: 244 KFYIKEAHEPGEVVLEVKNLSGERF-ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFR 302
             Y     E G+V L+VK L G    E VSF + +GEILG  GLVGAGRTEL+  + G  
Sbjct: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314

Query: 303 PKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSL---PSLDRI 359
            +R G + +  K +++  P DAI  G+ L PEDRKK G+I + S+  N+++   PS   +
Sbjct: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374

Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419
             G  +    E+  AD  IK+  ++     +K++YLSGGNQQK +L +WL++  K+L+LD
Sbjct: 375 --GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 432

Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479
           EPTRGID+GAKAEIY+I+  LA +G+ VI++SS+L EV+ +SDRI V+  G + G +   
Sbjct: 433 EPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRD 492

Query: 480 EASQEKVMKLA 490
           +A++  +++LA
Sbjct: 493 QANESNLLQLA 503



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 57/233 (24%), Positives = 116/233 (49%), Gaps = 8/233 (3%)

Query: 15  PGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPS 74
           PG+H  + VS + + GE+  + G  GAG++ L+++++G+ +  EG ++   + ++   P 
Sbjct: 277 PGLH--EPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLRSPR 334

Query: 75  EAINAGIVTVFQELS---VMDNLSVAENIFMGDEEKR---GIFIDYKKMYREAEKFMKEE 128
           +AI AG++   ++     ++   SV ENI +         G  +        A+K +K  
Sbjct: 335 DAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQIKSL 394

Query: 129 FGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLK 188
                   +K+   S   QQ   + R +    KVL+LDEPT  +      ++++++ +L 
Sbjct: 395 KVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLA 454

Query: 189 EKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
             G+A+I +S  L E+  I D++ VL +G   G  S +   +  ++++ + R+
Sbjct: 455 ADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQ 507


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: 695
Number of extensions: 34
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: 514
Length adjustment: 34
Effective length of query: 460
Effective length of database: 480
Effective search space:   220800
Effective search space used:   220800
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