GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA 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_00965 AO356_00965 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00965
          Length = 517

 Score =  343 bits (879), Expect = 1e-98
 Identities = 190/474 (40%), Positives = 288/474 (60%), Gaps = 3/474 (0%)

Query: 20  LKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINA 79
           L  +++    GEV A+ GENGAGKSTL KII G+  P  G++ ++G+  R    ++A   
Sbjct: 24  LTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEEL 83

Query: 80  GIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEIDPEEKL 139
           G+  V QEL+++  LSVAEN+F+ +    G +I  K++ + A + M +     IDP+  +
Sbjct: 84  GVRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAIEAMAQVGLDAIDPDTLV 143

Query: 140 GKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFISH 199
           G+  I  QQMVEIAR +     VLILDEPT+ LT +E E LFE +  L+ +GVAII+ISH
Sbjct: 144 GELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYISH 203

Query: 200 RLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEKFYIKEAHEPGEVVLE 259
           RLEE+  +  +++VLRDG  +  + + N   E++V +MVGR+L +       + G   L 
Sbjct: 204 RLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVGRELGEHIDLGPRQIGAPALT 263

Query: 260 VKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYI--EGKRV 316
           VK L+  ++  +VSF +R GEI G +GL+GAGRTEL+  IFG  P   G + +    + V
Sbjct: 264 VKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADPADSGTVALGSPARVV 323

Query: 317 EINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADW 376
            I  P DA+  GI L+ EDRK  GL+L  SI  N++L ++  I     ++   E  LA  
Sbjct: 324 SIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALGNMPEISSAGLVNGSAELALAQR 383

Query: 377 AIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRI 436
            +    IR + P + V  LSGGNQQKVV+ +WL     +++ DEPTRGIDVGAK +IY +
Sbjct: 384 QVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRGIDVGAKFDIYAL 443

Query: 437 MSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLA 490
           + +L ++G  ++++SS+L E++ + DRI V+S G+L    +    +Q+ ++  A
Sbjct: 444 LGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLAAA 497



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 5/225 (2%)

Query: 270 NVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGI 329
           +++ +L RGE+L   G  GAG++ L + I G      G++  +G+         A E G+
Sbjct: 26  DINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEELGV 85

Query: 330 GLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPD 389
            +V ++   L L+  +S+  N+ L +L     G +IS K+ ++ A  A+    +    PD
Sbjct: 86  RMVMQE---LNLLPTLSVAENLFLDNLP--SHGGWISRKQLRKAAIEAMAQVGLDAIDPD 140

Query: 390 RKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIM 449
             V  L  G+QQ V +A+ L     +LILDEPT  +       ++  +++L   GV +I 
Sbjct: 141 TLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIY 200

Query: 450 ISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           IS  L E+ +++ RIAV+  G L  +        E+++ L  G E
Sbjct: 201 ISHRLEELARVAQRIAVLRDGNLVCVEPMANYDSEQLVTLMVGRE 245


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: 584
Number of extensions: 29
Number of successful extensions: 7
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: 517
Length adjustment: 34
Effective length of query: 460
Effective length of database: 483
Effective search space:   222180
Effective search space used:   222180
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