GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:14809
          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:

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