GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylG in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410
          Length = 514

 Score =  375 bits (964), Expect = e-108
 Identities = 197/489 (40%), Positives = 313/489 (64%), Gaps = 4/489 (0%)

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

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124
            +   +   +++I +G+  + QEL ++  ++VAEN+F+G        I+   + ++A   
Sbjct: 76  EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALAC 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 ++ T + +  LT +++V  MVGR ++
Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQ 254

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

Query: 303 PKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK- 361
               G + + G+ ++++ P DAI  GI L PEDRKK G++ + S+  N+++ +       
Sbjct: 315 RNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTF 374

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

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

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



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 57/225 (25%), Positives = 114/225 (50%), Gaps = 6/225 (2%)

Query: 23  VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82
           VS E + GE+  + G  GAG++ L ++++G+ +   G +   GR ++ + P +AI AGI+
Sbjct: 283 VSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPRDAIAAGIL 342

Query: 83  TVFQELS---VMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEI---DPE 136
              ++     ++   SVAENI +        F    +   E +   K+   +++   +  
Sbjct: 343 LCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAA 402

Query: 137 EKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIF 196
           +K+   S   QQ   + R +    KVL+LDEPT  +      ++++++ +L   G+A+I 
Sbjct: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIV 462

Query: 197 ISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
           +S  L E+  I D++ VL +G   G  + E   +  ++++ + R+
Sbjct: 463 VSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPRQ 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: 647
Number of extensions: 33
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.

Links

Downloads

Related tools

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