GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Pseudomonas fluorescens FW300-N2C3

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 AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20250 AO356_20250
           L-arabinose transporter ATP-binding protein
          Length = 514

 Score =  385 bits (990), Expect = e-111
 Identities = 199/489 (40%), Positives = 319/489 (65%), Gaps = 4/489 (0%)

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 ARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254

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

Query: 303 PKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK- 361
            +  G + + GK +++  P DAI  G+ L PEDRKK G+I + S+  N+++ +       
Sbjct: 315 RQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPAHSAL 374

Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421
           G  +    E+  AD  IK+  ++     +K++YLSGGNQQK +L +WL++  K+L+LDEP
Sbjct: 375 GCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434

Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481
           TRGID+GAKAEIY+I+  LA +G+ VI++SS+L EV+ +SDRI V+  G + G +   +A
Sbjct: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494

Query: 482 SQEKVMKLA 490
           ++  +++LA
Sbjct: 495 NESNLLQLA 503



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 61/243 (25%), Positives = 121/243 (49%), Gaps = 10/243 (4%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           L+VKS+    PG+   + VS + + GE+  + G  GAG++ L ++++G+ +  EG ++  
Sbjct: 269 LQVKSLLG--PGLR--EPVSFQVHKGEILGLFGLVGAGRTELFRLLSGLERQSEGSLVLH 324

Query: 65  GRGVRWNHPSEAINAGIVTVFQELS---VMDNLSVAENIFMGDEEKR---GIFIDYKKMY 118
           G+ ++   P +AI AG++   ++     ++   SV ENI +         G  +      
Sbjct: 325 GKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPAHSALGCLLRGDWER 384

Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178
             A+K +K          +K+   S   QQ   + R +    KVL+LDEPT  +      
Sbjct: 385 GNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKA 444

Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           ++++++ +L   G+A+I +S  L E+  I D++ VL +G   G  S +   +  ++++ +
Sbjct: 445 EIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLAL 504

Query: 239 GRK 241
            R+
Sbjct: 505 PRQ 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: 679
Number of extensions: 32
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