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

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969 L-arabinose transport
           ATP-binding protein AraG (TC 3.A.1.2.2)
          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 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