GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:350322
          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.

Links

Downloads

Related tools

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