GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylT in Bacteroides thetaiotaomicron VPI-5482

Align D-xylose-proton symporter (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)

Query= CharProtDB::CH_109760
         (491 letters)



>FitnessBrowser__Btheta:350322
          Length = 484

 Score =  448 bits (1152), Expect = e-130
 Identities = 240/489 (49%), Positives = 330/489 (67%), Gaps = 37/489 (7%)

Query: 9   YIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGC 68
           Y++SIT VA LGGLLFGYDTAVISG  + L   F++  +   +    + G   +SALIGC
Sbjct: 12  YLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKV--MHGITSSSALIGC 69

Query: 69  IIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPE 128
           ++GGAL G  ++R GRR+SL++AAVLFF+S +GS +PE+ F      N + + +A     
Sbjct: 70  VLGGALSGVFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPN-MDLLIA----- 123

Query: 129 FVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARS 188
           F +YR++GGIGVGLAS + PMYIAE+AP++IRG LVS NQFAIIFG L+VY VNY I   
Sbjct: 124 FNLYRVLGGIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGD 183

Query: 189 G-------DAS-----------WLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSR 230
                   DA+           W   +GWRYMF SE  PA  F +LL+ VP++PR+L+  
Sbjct: 184 HQNPIILKDAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLV 243

Query: 231 GKQEQAEGILRKIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQF 290
            ++E+A  IL KI G   A + + +IK +     +   +L  +GV VIVIG++LS+FQQ 
Sbjct: 244 QQEEKAYTILEKINGKKKAQEILNDIKATAQEKTE---KLFTYGVTVIVIGILLSVFQQA 300

Query: 291 VGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGAL 350
           +GIN VLYYAP +F+  GA     ++QT+I+G++N+ FT++AI TVD+FGRKPL IIG++
Sbjct: 301 IGINAVLYYAPRIFENAGAEGG-GMMQTVIMGIVNIIFTLVAIFTVDRFGRKPLLIIGSI 359

Query: 351 GMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAI 410
           GMA+G F++         G++ +LS++ Y A F MSWGP+CWVL+SEIFPN IRGKA+AI
Sbjct: 360 GMAVGAFAVAMCDSMAIKGVLPVLSIIVYAAFFMMSWGPICWVLISEIFPNTIRGKAVAI 419

Query: 411 AVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKT 470
           AVA QW+ NY VS TFP +         F   F+Y +YG + V AA+F+W++VPETKGKT
Sbjct: 420 AVAFQWIFNYIVSSTFPAL-------YDFSPMFAYSLYGIICVAAAIFVWRWVPETKGKT 472

Query: 471 LEELEALWE 479
           LE++  LW+
Sbjct: 473 LEDMSKLWK 481


Lambda     K      H
   0.326    0.140    0.433 

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: 679
Number of extensions: 34
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: 491
Length of database: 484
Length adjustment: 34
Effective length of query: 457
Effective length of database: 450
Effective search space:   205650
Effective search space used:   205650
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:

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