GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG in Pseudomonas fluorescens FW300-N2E3

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 AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_20820 AO353_20820 sugar ABC
           transporter ATP-binding protein
          Length = 517

 Score =  348 bits (893), Expect = e-100
 Identities = 200/490 (40%), Positives = 293/490 (59%), Gaps = 4/490 (0%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +L V  I K +     L G+ +    GEV A+ GENGAGKSTL KII G+  P  G++ +
Sbjct: 9   VLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEK 123
           +GR  R    ++A   GI  V QEL+++  LSVAEN+F+ +    G +I  K++ + A  
Sbjct: 68  QGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRKAAIA 127

Query: 124 FMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEV 183
            M +     IDP+  +G+  I  QQMVEIAR +     VLILDEPT+ LT +E E LFE 
Sbjct: 128 AMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQ 187

Query: 184 VKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243
           +  L+ +GVAII+ISHRLEE+  +  +++VLRDG  +  + + N   E++V +MVGR+L 
Sbjct: 188 ITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRELG 247

Query: 244 KFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFR 302
           +         G   L VK LS  ++  +VSF +R GEI G +GL+GAGRTEL+  IFG  
Sbjct: 248 EHIDLGPRHIGAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGAD 307

Query: 303 PKRGGEIYI--EGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360
               G + +    + V I  P DA+  GI L+ EDRK  GL+L  SI  N++L ++  I 
Sbjct: 308 AADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPVIS 367

Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420
            G  ++   E  LA   I    IR + P + V  LSGGNQQKVV+ +WL  +  +L+ DE
Sbjct: 368 SGGIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVLLFDE 427

Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480
           PTRGIDVGAK +IY ++ +L ++G  ++++SS+L E++ + DRI V+S G+L    +   
Sbjct: 428 PTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDS 487

Query: 481 ASQEKVMKLA 490
            +Q+ ++  A
Sbjct: 488 WTQDDLLAAA 497



 Score = 87.8 bits (216), Expect = 8e-22
 Identities = 66/224 (29%), Positives = 111/224 (49%), Gaps = 5/224 (2%)

Query: 271 VSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIG 330
           +  +L RGE+L   G  GAG++ L + I G      G++  +G+         A E GI 
Sbjct: 27  IDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGRDYRPGSRTQAEELGIR 86

Query: 331 LVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDR 390
           +V ++   L L+  +S+  N+ L +L     G +IS K+ ++ A  A+    +    PD 
Sbjct: 87  MVMQE---LNLLPTLSVAENLFLDNLP--SNGGWISRKQLRKAAIAAMAQVGLDAIDPDT 141

Query: 391 KVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMI 450
            V  L  G+QQ V +A+ L     +LILDEPT  +       ++  +++L   GV +I I
Sbjct: 142 LVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYI 201

Query: 451 SSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494
           S  L E+ +++ RIAV+  G L  +      + E+++ L  G E
Sbjct: 202 SHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRE 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: 575
Number of extensions: 28
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 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