GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcba in Escherichia coli BW25113

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate 15223 b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)

Query= BRENDA::P45604
         (651 letters)



>FitnessBrowser__Keio:15223
          Length = 477

 Score =  382 bits (982), Expect = e-110
 Identities = 203/485 (41%), Positives = 307/485 (63%), Gaps = 34/485 (7%)

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

Query: 57  AIGVASSWSKDNAGSAALAGAVGYFVMTKAMVTINPEI--------------NMGVLAGI 102
           AIGVA  ++ +N G +ALA  V Y +M K M  + P +              + GVL GI
Sbjct: 64  AIGVALGFT-NNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGGI 122

Query: 103 ITGLVAGAVYNRWAGIKLPDFLSFFGGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSG 162
           I+G +A  ++NR+  IKLP++L FF GKRFVPI +G   +    +  ++WPP+  AI + 
Sbjct: 123 ISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQTF 182

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

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

Query: 282 FLFLFLAPLLYLLHAVLTGISLFIATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLL 341
           F F+F+AP+LY++HA+L G++  I   LG+  G SFS G ID+++   L   S  +W+  
Sbjct: 302 FSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIV---LSGNSSKLWLFP 358

Query: 342 VMGVVFFFVYFLLFSAVIRMFNLKTPGREDKAADVVTEEANSNTEEGLTQLATSYIAAVG 401
           ++G+ +  VY+ +F  +I+  +LKTPGRED      TE+A +    G +++A + +AA G
Sbjct: 359 IVGIGYAIVYYTIFRVLIKALDLKTPGRED-----ATEDAKAT---GTSEMAPALVAAFG 410

Query: 402 GTDNLKAIDACITRLRLTVGDSAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDE 461
           G +N+  +DACITRLR++V D +KV+ A  K+LGA+GVV +    +Q I G K++++  E
Sbjct: 411 GKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVV-VAGSGVQAIFGTKSDNLKTE 469

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


Lambda     K      H
   0.323    0.138    0.406 

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: 756
Number of extensions: 40
Number of successful extensions: 8
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: 651
Length of database: 477
Length adjustment: 36
Effective length of query: 615
Effective length of database: 441
Effective search space:   271215
Effective search space used:   271215
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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