GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Escherichia coli BW25113

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 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Keio:17809
          Length = 501

 Score =  434 bits (1117), Expect = e-126
 Identities = 225/494 (45%), Positives = 333/494 (67%), Gaps = 3/494 (0%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           M+ +L++K I K FPGV AL G ++  YPG V A+VGENGAGKST+MK++ G+Y  D G 
Sbjct: 1   MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE-EKRGIFIDYKKMYR 119
           +++ G+   +  P  +  AGI  + QEL+++  L++AENIF+G E   R   ID+K MY 
Sbjct: 61  LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120

Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179
           EA+K + +   +    ++ +G  SI  QQMVEIA+ +  ++KV+I+DEPT +LT  ETE 
Sbjct: 121 EADKLLAK-LNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETES 179

Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239
           LF V++ LK +G  I++ISHR++EIFEICD V+V RDG++I    + +LT++ ++EMMVG
Sbjct: 180 LFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVG 239

Query: 240 RKLEKFYIKEAHEPGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299
           RKLE  Y      PG++ L+V NL G    +VSF+LR+GEILG +GL+GAGRTELM+ ++
Sbjct: 240 RKLEDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLY 299

Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359
           G  P+  G + ++G  V    P D +  GI  + EDRK+ GL+L MS+  N+SL +L   
Sbjct: 300 GALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359

Query: 360 KK-GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILIL 418
            + G  +    E++     I+ F+++    ++ +  LSGGNQQKV +A+ L  +PK+LIL
Sbjct: 360 SRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419

Query: 419 DEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDA 478
           DEPTRG+DVGAK EIY++++Q   +G+ +I++SSE+PEVL MSDRI VM  G L+G    
Sbjct: 420 DEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTR 479

Query: 479 KEASQEKVMKLAAG 492
           ++A+QE +M  A G
Sbjct: 480 EQATQEVLMAAAVG 493



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 62/236 (26%), Positives = 116/236 (49%), Gaps = 17/236 (7%)

Query: 15  PGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPS 74
           PGV+    VS     GE+  + G  GAG++ LMK++ G      G +  +G  V    P 
Sbjct: 266 PGVN---DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322

Query: 75  EAINAGIVTVFQE---------LSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFM 125
           + +  GIV + ++         +SV +N+S+    +     + G  + +    +    F+
Sbjct: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS---RAGGSLKHADEQQAVSDFI 379

Query: 126 KEEFGIEIDP-EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184
           +  F ++    E+ +G  S   QQ V IAR +  + KVLILDEPT  +     +++++++
Sbjct: 380 RL-FNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLI 438

Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
              K  G++II +S  + E+  + D++ V+ +G   G  + E  T+E ++   VG+
Sbjct: 439 NQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494


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: 663
Number of extensions: 33
Number of successful extensions: 8
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: 501
Length adjustment: 34
Effective length of query: 460
Effective length of database: 467
Effective search space:   214820
Effective search space used:   214820
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