GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galP 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)



>FitnessBrowser__Btheta:349964
          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:

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