GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PLT5 in Bacteroides thetaiotaomicron VPI-5482

Align Polyol (xylitol):H+ symporter, PLT4 (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)

Query= TCDB::Q1XF07
         (519 letters)



>lcl|FitnessBrowser__Btheta:350322 BT0794 D-xylose-proton symporter
           (D-xylose transporter) (NCBI ptt file)
          Length = 484

 Score =  194 bits (492), Expect = 8e-54
 Identities = 154/509 (30%), Positives = 247/509 (48%), Gaps = 78/509 (15%)

Query: 32  YAFACAMLASMTSILLGYDIGVMSGAAIYIKRD-LKVSDVKI-EILLGIINLYSLIGSGL 89
           Y ++   +A +  +L GYD  V+SGA   ++   L  SD +  +++ GI +  +LIG  L
Sbjct: 12  YLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGITSSSALIGCVL 71

Query: 90  AGRTS----DWIGRRYTIVFAGAIFFVGALLMGFSPNYWFLMFG-------------RFI 132
            G  S      +GRR ++  A  +FF+ AL   + P   F  +G             R +
Sbjct: 72  GGALSGVFASRLGRRNSLRLAAVLFFLSAL-GSYYPEVLFFEYGKPNMDLLIAFNLYRVL 130

Query: 133 AGIGIGYALMIAPVYTAEVSPASSRGFLTSFPEVFINGGILLGYISNF------------ 180
            GIG+G A  + P+Y AE++P++ RG L S  +  I  G+L+ Y  N+            
Sbjct: 131 GGIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGDHQNPIIL 190

Query: 181 --AFSKLSLKV---------GWRMMLGVGALPSVILGVGVLAMPESPRWLVMRGRLGDAI 229
             A   LS+           GWR M G  A P+   G+ +  +P++PR+LV+  +   A 
Sbjct: 191 KDAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLVQQEEKAY 250

Query: 230 KVLNKTSDSPEEAQLRLADIKRAAGIPESCTDDVVEVSKRSTGEGVWKELFLYPTPAIRH 289
            +L K +   ++AQ  L DIK                   +T +   ++LF Y       
Sbjct: 251 TILEKINGK-KKAQEILNDIK-------------------ATAQEKTEKLFTYGVT---- 286

Query: 290 IVIAALGIHFFQQASGIDAVVLYSPTIFEKAGIKSDTDKLLATVAVGFVKTCFILVATFM 349
           +++  + +  FQQA GI+AV+ Y+P IFE AG  ++   ++ TV +G V   F LVA F 
Sbjct: 287 VIVIGILLSVFQQAIGINAVLYYAPRIFENAG--AEGGGMMQTVIMGIVNIIFTLVAIFT 344

Query: 350 LDRIGRRPLLLTSVGGMVLSLLTLGTSLTIIDRSDTKVTWAVGLSIATVLSYVATFSIGA 409
           +DR GR+PLL+    GM +    +          D+     V L + +++ Y A F +  
Sbjct: 345 VDRFGRKPLLIIGSIGMAVGAFAVAMC-------DSMAIKGV-LPVLSIIVYAAFFMMSW 396

Query: 410 GPITWVYSSEIFPLRLRAQGCAMGVVVNRVTSGVISMTFLSLSKGITIGGAFFLFGGIAI 469
           GPI WV  SEIFP  +R +  A+ V    + + ++S TF +L    +   A+ L+G I +
Sbjct: 397 GPICWVLISEIFPNTIRGKAVAIAVAFQWIFNYIVSSTFPAL-YDFSPMFAYSLYGIICV 455

Query: 470 CGWIFFYTMLPETRGKTLEDMEGSFGQSK 498
              IF +  +PET+GKTLEDM   + ++K
Sbjct: 456 AAAIFVWRWVPETKGKTLEDMSKLWKKNK 484


Lambda     K      H
   0.323    0.140    0.414 

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: 601
Number of extensions: 40
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 519
Length of database: 484
Length adjustment: 34
Effective length of query: 485
Effective length of database: 450
Effective search space:   218250
Effective search space used:   218250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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