GapMind for catabolism of small carbon sources

 

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

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate 349964 BT0436 arabinose-proton symporter (NCBI ptt file)

Query= SwissProt::P96710
         (464 letters)



>lcl|FitnessBrowser__Btheta:349964 BT0436 arabinose-proton symporter
           (NCBI ptt file)
          Length = 468

 Score =  325 bits (832), Expect = 3e-93
 Identities = 180/460 (39%), Positives = 272/460 (59%), Gaps = 14/460 (3%)

Query: 19  SMGFVILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVG 78
           + G++I +S  A LGG L+GYDTAVISG I  +  L+ L    +G  +   +IG +VGV 
Sbjct: 6   NFGYLIFLSVVAALGGFLFGYDTAVISGTIAQVTQLFQLDTLQQGWYVGCALIGSIVGVL 65

Query: 79  ISGFLSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYI 138
            +G LSD+ GR+  ++ +A LF+ SA+  A+S D + L++ RIIGG+GIG+ S +S  YI
Sbjct: 66  FAGILSDKLGRKMTMIISATLFSTSALGCAISADFTQLVVYRIIGGVGIGVVSIVSPLYI 125

Query: 139 TEAAPPAIRGSLSSLYQLFTILGISATYFIN---LAVQRSG---TYEW----GVHTGWRW 188
           +E A    RG L SLYQL   +G    Y IN   LA   SG   + +W     V   WR 
Sbjct: 126 SEVAVAQYRGRLVSLYQLAVTVGFLGAYLINYQLLAYAESGNQLSMDWLNKIFVTEVWRG 185

Query: 189 MLAYGMVPSVIFFLVLLVVPESPRWLAKAGKTNEALKILTRI-NGETVAKEELKNIENSL 247
           ML    +P+V+FF+++  +PESPRWL   GK  +A+ IL RI N  + A  +LK  ++ L
Sbjct: 186 MLGMETLPAVLFFIIIFFIPESPRWLIVRGKEEKAVNILERIYNSVSEAASQLKETKSVL 245

Query: 248 KIEQMGSLSQLFKPGLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTT 307
             E     + L KPG+ KA++IG+ +A+  Q +G+NA+ YYGP IF+  G          
Sbjct: 246 TSETKSEWAMLMKPGIFKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGGDSLFYQ 305

Query: 308 CIVGVVEVIFTVIAVLLIDKVGRKKLMSIGSAFMAIFMILIGTSFYFELT---SGIMMIV 364
            +VG+V  + TV+A+++ID+VGRK+L+  G + M + ++LIG  F F  +   S + ++V
Sbjct: 306 VLVGLVNTLTTVLALVIIDRVGRKQLVYYGVSGMVVSLLLIGVYFLFGDSWGVSSLFLLV 365

Query: 365 LILGFVAAFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMIDSFG 424
             L +V    VS+  + ++++SE++P  +R  A  IA   LW   + IGQ  P M+ +  
Sbjct: 366 FFLFYVFCCAVSICAVVFVLLSEMYPTKVRGLAMSIAGFALWIGTYLIGQLTPWMLQNLT 425

Query: 425 LAYTFWIFAVINILCFLFVVTICPETKNKSLEEIEKLWIK 464
            A TF++FAV+ +   L V  + PET  KSLEEIE+ W +
Sbjct: 426 PAGTFFLFAVMCVPYMLIVWKLVPETTGKSLEEIERYWTR 465


Lambda     K      H
   0.327    0.142    0.425 

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: 609
Number of extensions: 27
Number of successful extensions: 5
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: 464
Length of database: 468
Length adjustment: 33
Effective length of query: 431
Effective length of database: 435
Effective search space:   187485
Effective search space used:   187485
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 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