GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Btheta:350322 BT0794 D-xylose-proton symporter
           (D-xylose transporter) (NCBI ptt file)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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