GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Escherichia coli BW25113

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate 16276 b2167 fused fructose-specific PTS enzymes: IIBcomponent/IIC components (NCBI)

Query= TCDB::Q1LZ59
         (655 letters)



>lcl|FitnessBrowser__Keio:16276 b2167 fused fructose-specific PTS
           enzymes: IIBcomponent/IIC components (NCBI)
          Length = 563

 Score =  332 bits (852), Expect = 2e-95
 Identities = 207/531 (38%), Positives = 300/531 (56%), Gaps = 51/531 (9%)

Query: 131 DKLRQVTNPDDVINLFNATEEEKKEATPAA---PVADSHDF-LVAVTACTTGIAHTYMAE 186
           D  R V +P+  + L  A    K    P A   PVA S    +VAVTAC TG+AHT+MA 
Sbjct: 66  DISRAVAHPE--LFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTFMAA 123

Query: 187 EALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAVEMDRFNGKPLISR 246
           EA++ +A + G  +KVET G+ G GN +T +++  A  VI+AAD  V++ +F GKP+   
Sbjct: 124 EAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPMYRT 183

Query: 247 PVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAGLGSAFYKHLMSGVSQMLP 306
                +KK  + ++  +        A  +  ++  S  E AG     Y+HL++GVS MLP
Sbjct: 184 STGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGA----YRHLLTGVSYMLP 239

Query: 307 FVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAY 366
            V+ GG+ IALSF           +L+        AA+    G +AF  M+PV A YIA+
Sbjct: 240 MVVAGGLCIALSFAFGIEAFKEPGTLA--------AALMQIGGGSAFALMVPVLAGYIAF 291

Query: 367 SIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGG 426
           SIA++PGL  G + G +A +                     TG  SGF+G +  GFLAG 
Sbjct: 292 SIADRPGLTPGLIGGMLAVS---------------------TG--SGFIGGIIAGFLAGY 328

Query: 427 VILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLF-VNIPMAAINTALYNFLGNLS 485
           +  ++   L  +P+S+E +K IL+ PL+  LV G  M++ +  P+A I   L ++L  + 
Sbjct: 329 IAKLISTQLK-LPQSMEALKPILIIPLISSLVVGLAMIYLIGKPVAGILEGLTHWLQTMG 387

Query: 486 GGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPL 545
             +AVLLG I+GGMM  DMGGP NKAAY FG   L+           MA++MA GMVPPL
Sbjct: 388 TANAVLLGAILGGMMCTDMGGPVNKAAYAFGVGLLSTQTYGP-----MAAIMAAGMVPPL 442

Query: 546 AVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGA 605
           A+ +AT++ + KF + + + G   +V+GL FI+EGAIPF A DP R +P  IVG A+TGA
Sbjct: 443 AMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIPFAARDPMRVLPCCIVGGALTGA 502

Query: 606 LVGLSGIKLMAPHGGIFVIALTS--NPLL-YLLYIAVGAVIAGILFGSLRK 653
           +    G KLMAPHGG+FV+ +     P+L YL+ I  G ++AG+ +  L++
Sbjct: 503 ISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAGTLVAGLAYAFLKR 553


Lambda     K      H
   0.320    0.137    0.381 

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: 907
Number of extensions: 59
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: 655
Length of database: 563
Length adjustment: 37
Effective length of query: 618
Effective length of database: 526
Effective search space:   325068
Effective search space used:   325068
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 (21.8 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