Alignments for a candidate for malEIICBA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for malEIICBA in Escherichia coli BW25113

Align PTS system, IIABC components (characterized, see rationale)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)

Query= uniprot:Q836Y6
         (722 letters)



>FitnessBrowser__Keio:14809
          Length = 648

 Score =  317 bits (813), Expect = 9e-91
 Identities = 233/722 (32%), Positives = 354/722 (49%), Gaps = 104/722 (14%)

Query: 9   FWQKFGKALMVVVAVMPAAGLMISIGKSLPLIDPNLGLLVTTGGVLESIGWAIIGNLHLL 68
           F+Q+ G+AL + +AV+P A L++  G+   L   N+  +   GG       AI  NL L+
Sbjct: 6   FFQRLGRALQLPIAVLPVAALLLRFGQPDLL---NVAFIAQAGG-------AIFDNLALI 55

Query: 69  FALAIGGSWAKDRAGGAFAAGISFVLINRITGAIFGVTNEMLADEQAFTHTLFGTKIMVK 128
           FA+ +  SW+KD AG A  AG                                G  ++ K
Sbjct: 56  FAIGVASSWSKDSAGAAALAGA------------------------------VGYFVLTK 85

Query: 129 GFFTSVLEAPALNMGVFVGIIAGFVGAMAYNKYYNYRKLPDALSFFNGKRFVPFVVILWS 188
              T     P +NMGV  GII G VG  AYN++ +  KLPD LSFF GKRFVP     + 
Sbjct: 86  AMVTI---NPEINMGVLAGIITGLVGGAAYNRWSDI-KLPDFLSFFGGKRFVPIATGFFC 141

Query: 189 TIVSIALALIWPNIQAGINNFGLWIAQSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPI 248
            +++     +WP +Q  I+  G WI     SA  L   ++G + RLL+P GLH +L   I
Sbjct: 142 LVLAAIFGYVWPPVQHAIHAGGEWIV----SAGALGSGIFGFINRLLIPTGLHQVLNT-I 196

Query: 249 NYTQLGGTYEILSGAQAGTQVFGQDPLWLAWATDLVNLKGAGDMSKYQFVLENWTPARFK 308
            + Q+G   E  + A  GT   G            +N   AGD +   F+      + F 
Sbjct: 197 AWFQIG---EFTNAA--GTVFHGD-----------INRFYAGDGTAGMFM------SGFF 234

Query: 309 VGQMIGSSGILMGMALAMYRNVDADKKAKYKSMYFSAALAVFLTGVTEPLEFMFMFAAVP 368
              M G    L G ALAMY     +++     M  S A+  FLTGVTEPLEF+FMF A  
Sbjct: 235 PIMMFG----LPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPL 290

Query: 369 LYVIYAVIQGAAFAMADILPLRV---HSFGNIE--LLTRTPLAIKAGLGGDLINFVLMVI 423
           LY+++A++ G +  +A +L +      S G I+  L+   P A +     ++   ++M +
Sbjct: 291 LYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQ-----NVWMLLVMGV 345

Query: 424 IFGVVTYFLANFLIKKFNYATPGRNGNYDNDNSEEIASGAAGSGVVDQQIAQIVYLLGGK 483
           IF  + + + + +I+ FN  TPGR    D   +EE  S       + Q     +  +GG 
Sbjct: 346 IFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEG--LTQLATNYIAAVGGT 403

Query: 484 QNIKEVDACMTRLRVSVKDREKVGSEEAWKRAGAMGLI-VKDNGVQAVYGPKADVLKSDI 542
            N+K +DAC+TRLR++V D  +V ++   KR GA G++ +    +Q + G KA+ +   +
Sbjct: 404 DNLKAIDACITRLRLTVADSARV-NDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAM 462

Query: 543 EDLLASGVDIPEPVIAESTAGVPTTNFLGKKK----------DFVAVATGEVIPMAQVND 592
           + ++A G     PV A S    P T     K           + V+  TG+V+ + QV D
Sbjct: 463 KKVVARG-----PVAAASAEATPATAAPVAKPQAVPNAVSIAELVSPITGDVVALDQVPD 517

Query: 593 PVFSQKMMGDGFAVKPLEGEVVAPISGKVLSVFPSKHAIGLQTEEGIEVLVHMGIDTVEM 652
             F+ K +GDG AVKP +  VV+P +G ++ +F + HA  L+TE+G E++VHMGIDTV +
Sbjct: 518 EAFASKAVGDGVAVKPTDKIVVSPAAGTIVKIFNTNHAFCLETEKGAEIVVHMGIDTVAL 577

Query: 653 ATPAFESFVKEGQSLKAGTKLAKMNLDVIEQAGKETTIIVAFTNSDKVEQVVINQLGTTT 712
               F+  V+EG  + AG  + +M+LD +    +     V  +N D    ++I   G   
Sbjct: 578 EGKGFKRLVEEGAQVSAGQPILEMDLDYLNANARSMISPVVCSNIDDFSGLIIKAQGHIV 637

Query: 713 AG 714
           AG
Sbjct: 638 AG 639


Lambda     K      H
   0.322    0.138    0.404 

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: 1121
Number of extensions: 62
Number of successful extensions: 9
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: 722
Length of database: 648
Length adjustment: 39
Effective length of query: 683
Effective length of database: 609
Effective search space:   415947
Effective search space used:   415947
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 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