GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsG in Escherichia coli BW25113

Align PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)

Query= SwissProt::P37439
         (477 letters)



>lcl|FitnessBrowser__Keio:14809 b0679 fused N-acetyl glucosamine
           specific PTS enzyme: IIC, IIB , and IIA components
           (NCBI)
          Length = 648

 Score =  373 bits (958), Expect = e-108
 Identities = 202/485 (41%), Positives = 302/485 (62%), Gaps = 34/485 (7%)

Query: 4   NAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIF 63
           N     Q++G++L LP++VLP+A +LL  G  +   +  +     A+AGG++F N+ LIF
Sbjct: 2   NILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFI-----AQAGGAIFDNLALIF 56

Query: 64  AIGVALGFTNND-GVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIAAKHLADTGVLGGI 122
           AIGVA  ++ +  G +ALA  V Y ++ K M  + P +              + GVL GI
Sbjct: 57  AIGVASSWSKDSAGAAALAGAVGYFVLTKAMVTINPEI--------------NMGVLAGI 102

Query: 123 ISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFVWPPIGTAIQAF 182
           I+G +    +NR+  IKLP++L FF GKRFVPI +G   +    +  +VWPP+  AI A 
Sbjct: 103 ITGLVGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAG 162

Query: 183 SQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMA 242
            +W       +  GI+GFI R L+P GLH + N     QIGE+TNAAG VFHGDI R+ A
Sbjct: 163 GEWIVSAG-ALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYA 221

Query: 243 GDPTAGM-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIE 301
           GD TAGM +SG F   M+GLP AA+A++ +A  E R  VGG+++S A+T+FLTG+TEP+E
Sbjct: 222 GDGTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLE 281

Query: 302 FSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIV---LSGNSSKLWLFP 358
           F FMF+AP+LY++HA+L G++  +  LLG+  G SFS G ID+ +   L   S  +W+  
Sbjct: 282 FLFMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLL 341

Query: 359 IVGAGYAIVYYTVFRVLIKALDLKTPGREDTTDD---AKAGATSE-----MAPALVAAFG 410
           ++G  +  +Y+ VF ++I+  +LKTPGRED  D+    +A + +E     +A   +AA G
Sbjct: 342 VMGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVG 401

Query: 411 GKENITNLDACITRLRVSVADVAKVDQAGLKKLGAAGVV-VAGSGVQAIFGTKSDNLKTE 469
           G +N+  +DACITRLR++VAD A+V+    K+LGA+GVV +    +Q I G K++++   
Sbjct: 402 GTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDA 461

Query: 470 MDEYI 474
           M + +
Sbjct: 462 MKKVV 466


Lambda     K      H
   0.325    0.140    0.421 

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: 850
Number of extensions: 57
Number of successful extensions: 9
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: 477
Length of database: 648
Length adjustment: 36
Effective length of query: 441
Effective length of database: 612
Effective search space:   269892
Effective search space used:   269892
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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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