Alignments for a candidate for malEIICB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for malEIICB in Escherichia coli BW25113

Align The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)

Query= TCDB::Q63GK8
         (545 letters)



>FitnessBrowser__Keio:14809
          Length = 648

 Score =  235 bits (600), Expect = 3e-66
 Identities = 173/532 (32%), Positives = 265/532 (49%), Gaps = 87/532 (16%)

Query: 8   FWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHIL 67
           F+Q+ G+AL + +AV+P A L++  G+       D+  V  IA+     G AI  NL ++
Sbjct: 6   FFQRLGRALQLPIAVLPVAALLLRFGQ------PDLLNVAFIAQA----GGAIFDNLALI 55

Query: 68  FAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDLIVK 127
           FA+ +  SW+KD AG A  AL   V    +T A+  +N                      
Sbjct: 56  FAIGVASSWSKDSAGAA--ALAGAVGYFVLTKAMVTIN---------------------- 91

Query: 128 DYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIVWS 187
                    P +NMGV  GIITG +G   YN++ +  KLP  L+FF GKRFVP     + 
Sbjct: 92  ---------PEINMGVLAGIITGLVGGAAYNRWSDI-KLPDFLSFFGGKRFVPIATGFFC 141

Query: 188 TVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTIPM 247
            V A +   +WP +Q  ++  G WI     SA  +   ++G + RLL+P GLH +L   +
Sbjct: 142 LVLAAIFGYVWPPVQHAIHAGGEWIV----SAGALGSGIFGFINRLLIPTGLHQVLNT-I 196

Query: 248 NYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPARFK 307
            + ++G  +T    +  G V  G          D+N   A   T              F 
Sbjct: 197 AWFQIG-EFT----NAAGTVFHG----------DINRFYAGDGTAGM-----------FM 230

Query: 308 AGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIAPV 367
           +G        L G A AM+    KE+R     M LS A+  FLTGVTEP+EF+FMF+AP+
Sbjct: 231 SGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPL 290

Query: 368 LYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVN-AGLTRDLINFVIVSLVFFG 426
           LY+++A+ TG++  +A L+ +    F F        +M N    ++++   +++ ++FF 
Sbjct: 291 LYLLHALLTGISLFVATLLGIHA-GFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFA 349

Query: 427 LNFTLFNFLIKKFNLPTPGRAGNYIDNEDE--ASEGTGNVQDG--SLATKVIDLLGGKEN 482
           + F +F+ +I+ FNL TPGR     D EDE    E   N ++G   LAT  I  +GG +N
Sbjct: 350 IYFVVFSLVIRMFNLKTPGRE----DKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDN 405

Query: 483 IADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDK-GVQAVYGPKAD 533
           +  +DAC+TRLR+TV D      +   K+ GA G++  +K  +Q + G KA+
Sbjct: 406 LKAIDACITRLRLTVAD-SARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAE 456


Lambda     K      H
   0.325    0.140    0.416 

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: 799
Number of extensions: 40
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 545
Length of database: 648
Length adjustment: 37
Effective length of query: 508
Effective length of database: 611
Effective search space:   310388
Effective search space used:   310388
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 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
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