GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Bacteroides faecis MAJ27

Align Glucose facilitated diffusion protein (characterized)
to candidate WP_010538095.1 KCY_RS0116360 D-xylose transporter XylE

Query= SwissProt::P21906
         (473 letters)



>NCBI__GCF_000226135.1:WP_010538095.1
          Length = 484

 Score =  315 bits (808), Expect = 2e-90
 Identities = 180/494 (36%), Positives = 277/494 (56%), Gaps = 36/494 (7%)

Query: 2   SSESSQGLVTRLALIAAIGGLLFGYDSAVIAAIGTPVDIHFIAPRHLSATAAASLSGMVV 61
           ++E S+  +  +  +A +GGLLFGYD+AVI+     ++  F++           + G+  
Sbjct: 5   TNEGSKLYLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKV--MHGITS 62

Query: 62  VAVLVGCVTGSLLSGWIGIRFGRRGGLLMSSICFVAAGFGAALTEKLFGTGGSA----LQ 117
            + L+GCV G  LSG    R GRR  L ++++ F  +  G+   E LF   G      L 
Sbjct: 63  SSALIGCVLGGALSGIFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPNMDLLI 122

Query: 118 IFCFFRFLAGLGIGVVSTLTPTYIAEIAPPDKRGQMVSGQQMAIVTGALTGYIFTWLLA- 176
            F  +R L G+G+G+ S + P YIAEIAP + RG +VS  Q AI+ G L  Y   +L+  
Sbjct: 123 AFNLYRVLGGIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMG 182

Query: 177 -HFGSID----------------WVNASGWCWSPASEGLIGIAFLLLLLTAPDTPHWLVM 219
            H   I                 W    GW +   SE      F +LL   P TP +LV+
Sbjct: 183 DHQNPIILKDAAGVLSVSTESDMWTVQEGWRYMFGSEAFPAALFGMLLFFVPKTPRYLVL 242

Query: 220 KGRHSEASKILARLEPQADPNLTIQKIKAGFDKAMDKSSAGLFAFGITVVFAGVSVAAFQ 279
             +  +A  IL ++  +A     +  IKA   +  +K    +F +G+TV+  G+ ++ FQ
Sbjct: 243 VQQEEKAYSILEKINGKAKAREILNDIKATAQEKTEK----IFTYGVTVIVIGILLSVFQ 298

Query: 280 QLVGINAVLYYAPQMFQNLGFGADTALLQTISIGVVNFIFTMIASRVVDRFGRKPLLIWG 339
           Q +GINAVLYYAP++F+N G      ++QT+ +GVVN IFT++A   VDRFGRKPLLI G
Sbjct: 299 QAIGINAVLYYAPRIFENAG-AEGGGMMQTVIMGVVNIIFTLVAIFTVDRFGRKPLLIIG 357

Query: 340 ALGMAAMMAVLGCCFWFKVGGVLPLASVLLYIAVFGMSWGPVCWVVLSEMFPSSIKGAAM 399
           ++GMA     +  C    + GVLP+ S+++Y A F MSWGP+CWV++SE+FP++I+G A+
Sbjct: 358 SIGMAVGAFAVAMCDSMAIKGVLPVLSIIVYAAFFMMSWGPICWVLISEIFPNTIRGKAV 417

Query: 400 PIAVTGQWLANILVNFLFKVADGSPALNQTFNHGFSYLVFAALSILGGLIVARFVPETKG 459
            IAV  QW+ N +V+  F      PAL   F+  F+Y ++  + +   + V R+VPETKG
Sbjct: 418 AIAVAFQWIFNYIVSSTF------PAL-YDFSPMFAYSLYGIICVAAAIFVWRWVPETKG 470

Query: 460 RSLDEIEEMWRSQK 473
           ++L+++ ++W+  K
Sbjct: 471 KTLEDMSKLWKKNK 484


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: 536
Number of extensions: 27
Number of successful extensions: 7
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: 484
Length adjustment: 34
Effective length of query: 439
Effective length of database: 450
Effective search space:   197550
Effective search space used:   197550
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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