Alignments for a candidate for mglA in Escherichia coli BW25113

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:

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