GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Escherichia coli BW25113

Align Glucose facilitated diffusion protein (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)

Query= SwissProt::P21906
         (473 letters)



>lcl|FitnessBrowser__Keio:18059 b4031 D-xylose transporter (NCBI)
          Length = 491

 Score =  400 bits (1029), Expect = e-116
 Identities = 202/482 (41%), Positives = 300/482 (62%), Gaps = 11/482 (2%)

Query: 1   MSSESSQGLVTRLALIAAIGGLLFGYDSAVIAAIGTPVDIHFIAPRHLSATAAASLSGMV 60
           M+++ +   +  + L+A +GGLLFGYD+AVI+     ++  F+AP++LS +AA SL G  
Sbjct: 1   MNTQYNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFC 60

Query: 61  VVAVLVGCVTGSLLSGWIGIRFGRRGGLLMSSICFVAAGFGAALTEKLFGTGGSALQI-- 118
           V + L+GC+ G  L G+   RFGRR  L ++++ F  +G G+A  E  F +      +  
Sbjct: 61  VASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPV 120

Query: 119 --------FCFFRFLAGLGIGVVSTLTPTYIAEIAPPDKRGQMVSGQQMAIVTGALTGYI 170
                   F  +R + G+G+G+ S L+P YIAE+AP   RG++VS  Q AI+ G L  Y 
Sbjct: 121 YLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYC 180

Query: 171 FTWLLAHFGSIDWVNASGWCWSPASEGLIGIAFLLLLLTAPDTPHWLVMKGRHSEASKIL 230
             + +A  G   W+N  GW +  ASE +  + FL+LL T P++P WL+ +G+  +A  IL
Sbjct: 181 VNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGIL 240

Query: 231 ARLEPQADPNLTIQKIKAGFDKAMDKSSAGLFAFGITVVFAGVSVAAFQQLVGINAVLYY 290
            ++         +Q+IK   D    K+   L  FG+ V+  GV ++ FQQ VGIN VLYY
Sbjct: 241 RKIMGNTLATQAVQEIKHSLDHGR-KTGGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYY 299

Query: 291 APQMFQNLGFGADTALLQTISIGVVNFIFTMIASRVVDRFGRKPLLIWGALGMAAMMAVL 350
           AP++F+ LG   D ALLQTI +GV+N  FT++A   VD+FGRKPL I GALGMA  M  L
Sbjct: 300 APEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSL 359

Query: 351 GCCFWFKVGGVLPLASVLLYIAVFGMSWGPVCWVVLSEMFPSSIKGAAMPIAVTGQWLAN 410
           G  F+ +  G++ L S+L Y+A F MSWGPVCWV+LSE+FP++I+G A+ IAV  QWLAN
Sbjct: 360 GTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLAN 419

Query: 411 ILVNFLFKVADGSPALNQTFNHGFSYLVFAALSILGGLIVARFVPETKGRSLDEIEEMWR 470
             V++ F + D +  L   F++GFSY ++  + +L  L + +FVPETKG++L+E+E +W 
Sbjct: 420 YFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479

Query: 471 SQ 472
            +
Sbjct: 480 PE 481


Lambda     K      H
   0.327    0.140    0.434 

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: 613
Number of extensions: 25
Number of successful extensions: 3
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: 473
Length of database: 491
Length adjustment: 34
Effective length of query: 439
Effective length of database: 457
Effective search space:   200623
Effective search space used:   200623
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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