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

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_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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources