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 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Keio:18115
          Length = 510

 Score =  375 bits (962), Expect = e-108
 Identities = 209/504 (41%), Positives = 325/504 (64%), Gaps = 17/504 (3%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P + +  I K F  VHALK V++  YPGE+HA++GENGAGKSTLMK+++G+++P +G I 
Sbjct: 4   PYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTIT 63

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI----FIDYKKMY 118
                        A   GI  ++QELSV+D L+V EN+++G    + I     ID+++M 
Sbjct: 64  INNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWREM- 122

Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178
           R     M    G+++D +EK+   SI+ +QM+EIA+ +   AKV+I+DEPTSSLT KE +
Sbjct: 123 RVRAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVD 182

Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
            LF ++  L+++G AI++ISH+L EI  ICD+ +V++DG  + +  + +++ + IV +MV
Sbjct: 183 YLFLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMV 242

Query: 239 GRKLEKFY--IKE--AHEPGEVVLEVKNLSG---ERFENVSFSLRRGEILGFAGLVGAGR 291
           GR+L+  +  +KE  ++   E V EV+N++    ++  ++SFS+ RGEILGFAGLVG+GR
Sbjct: 243 GRELQNRFNAMKENVSNLAHETVFEVRNVTSRDRKKVRDISFSVCRGEILGFAGLVGSGR 302

Query: 292 TELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNV 351
           TELM  +FG   + GGEI + GK +    PLDA+++G+  + E R+  G     SI  N+
Sbjct: 303 TELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIAQNM 362

Query: 352 SLPSL--DRIKKGPFISFKR--EKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAK 407
           ++     D   KG    F    E+  A+   +   ++    ++ +  LSGGNQQKV+++K
Sbjct: 363 AISRSLKDGGYKGAMGLFHEVDEQRTAENQRELLALKCHSVNQNITELSGGNQQKVLISK 422

Query: 408 WLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVM 467
           WL   P+++I DEPTRGIDVGAKAEIY++M QLA +G  ++M+SSELPE++ + DRIAV 
Sbjct: 423 WLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITVCDRIAVF 482

Query: 468 SFGKLAGII-DAKEASQEKVMKLA 490
             G+L  I+ +  + S+E++M  A
Sbjct: 483 CEGRLTQILTNRDDMSEEEIMAWA 506



 Score = 78.2 bits (191), Expect = 6e-19
 Identities = 64/231 (27%), Positives = 119/231 (51%), Gaps = 12/231 (5%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRV-EINHPLDAIEQ 327
           ++V+ ++  GEI    G  GAG++ LM+ + G      G I I      +++H L A + 
Sbjct: 22  KSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTITINNISYNKLDHKL-AAQL 80

Query: 328 GIGLVPEDRKKLGLILIMSIMHNVSLPS--LDRIKKGPFISFKREKELADWAIKTFDIRP 385
           GIG++ ++   L +I  ++++ N+ +      +I     I ++  +  A   +    ++ 
Sbjct: 81  GIGIIYQE---LSVIDELTVLENLYIGRHLTKKICGVNIIDWREMRVRAAMMLLRVGLKV 137

Query: 386 AYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGV 445
              D KV  LS  ++Q + +AK L L  K++I+DEPT  +       ++ IM+QL KEG 
Sbjct: 138 DL-DEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDYLFLIMNQLRKEGT 196

Query: 446 GVIMISSELPEVLQMSDRIAVMSFGK--LAGIIDAKEASQEKVMKLAAGLE 494
            ++ IS +L E+ ++ DR  VM  G    +GI+   + S + +++L  G E
Sbjct: 197 AIVYISHKLAEIRRICDRYTVMKDGSSVCSGIV--SDVSNDDIVRLMVGRE 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: 722
Number of extensions: 28
Number of successful extensions: 9
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: 510
Length adjustment: 34
Effective length of query: 460
Effective length of database: 476
Effective search space:   218960
Effective search space used:   218960
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
the source code
instructions for running GapMind on your computer

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