GapMind for catabolism of small carbon sources

 

Aligments 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 15223 b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)

Query= TCDB::Q63GK8
         (545 letters)



>lcl|FitnessBrowser__Keio:15223 b1101 fused glucose-specific PTS
           enzymes: IIB component/IIC component (NCBI)
          Length = 477

 Score =  261 bits (666), Expect = 6e-74
 Identities = 178/537 (33%), Positives = 281/537 (52%), Gaps = 75/537 (13%)

Query: 10  QKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHILFA 69
           QK GK+L++ V+V+P AG+++ +G     SA        ++ VM + G ++  N+ ++FA
Sbjct: 10  QKVGKSLMLPVSVLPIAGILLGVG-----SANFSWLPAVVSHVMAEAGGSVFANMPLIFA 64

Query: 70  VAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDLIVKDY 129
           + +   +  +    A AA++A+           G+  + +A     V  + A ++  K  
Sbjct: 65  IGVALGFTNNDGVSALAAVVAY-----------GIMVKTMAVVAPLVLHLPAEEIASKHL 113

Query: 130 FTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIVWSTV 189
                     + GV  GII+G + A ++N++Y   KLP+ L FF GKRFVP +  + +  
Sbjct: 114 ---------ADTGVLGGIISGAIAAYMFNRFYRI-KLPEYLGFFAGKRFVPIISGLAAIF 163

Query: 190 TAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTIPMNY 249
           T +VLS +WP I S +  F +W A      P+VA  +YG +ER L+PFGLHH+  +P   
Sbjct: 164 TGVVLSFIWPPIGSAIQTFSQWAAYQN---PVVAFGIYGFIERCLVPFGLHHIWNVPFQM 220

Query: 250 TELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPARFKAG 309
               G YT    +  GQV  G  P ++A           GD  A              +G
Sbjct: 221 QI--GEYT----NAAGQVFHGDIPRYMA-----------GDPTAGK-----------LSG 252

Query: 310 QVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIAPVLY 369
             +     L   A A++ +   E RAK   + +SAAL  FLTG+TEPIEF FMF+AP+LY
Sbjct: 253 GFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILY 312

Query: 370 VVYAITTGLAFALADLINLR---VHAFGFIELITRTPMMVNAGLTRDLINFVIVSLVFFG 426
           +++AI  GLAF +  L+ +R     + G I+ I      V +G +  L  F IV + +  
Sbjct: 313 IIHAILAGLAFPICILLGMRDGTSFSHGLIDFI------VLSGNSSKLWLFPIVGIGYAI 366

Query: 427 LNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENIADV 486
           + +T+F  LIK  +L TPGR        ++A+E         +A  ++   GGKENI ++
Sbjct: 367 VYYTIFRVLIKALDLKTPGR--------EDATEDAKATGTSEMAPALVAAFGGKENITNL 418

Query: 487 DACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLKSDIQDML 543
           DAC+TRLRV+V D+  V  +A  K+ GA G++V   GVQA++G K+D LK+++ + +
Sbjct: 419 DACITRLRVSVADVSKV-DQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474


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: 652
Number of extensions: 34
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 545
Length of database: 477
Length adjustment: 34
Effective length of query: 511
Effective length of database: 443
Effective search space:   226373
Effective search space used:   226373
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: 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 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