GapMind for catabolism of small carbon sources

 

Alignments for a candidate for agcS in Bacteroides thetaiotaomicron VPI-5482

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 354002 BT4476 amino acid carrier protein (NCBI ptt file)

Query= TCDB::W0WFC6
         (449 letters)



>FitnessBrowser__Btheta:354002
          Length = 462

 Score =  272 bits (696), Expect = 1e-77
 Identities = 160/446 (35%), Positives = 253/446 (56%), Gaps = 11/446 (2%)

Query: 7   WVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISP 66
           ++ ++N ++W  ++++++LG  ++  +  +F+    L     LL +   K  +    +S 
Sbjct: 3   FINEINDILWTYILIIMLLGCAVWFSIRTRFVQFRMLREMIILLSESAGKGKQGEKHVSS 62

Query: 67  FQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKD 126
           FQA    +A+ VGTGN+AGVATAI +GGPGA+FWMW  AL+G ++ F E  LA  Y+ + 
Sbjct: 63  FQAFAITIASRVGTGNLAGVATAIAIGGPGAVFWMWVIALLGASSAFIESTLAQLYKIRG 122

Query: 127 ERNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLA-GFGIGNMVQVNSMADALEVSFGVP 185
            ++  VGGP Y +K GL  +  W+G  FA+   +  GF   N VQ N++  A E +FG  
Sbjct: 123 -KDSFVGGPAYYMKKGL--KQPWMGILFAVLISITFGFAF-NSVQSNTICAAAEHAFGFN 178

Query: 186 DWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLI 245
             V G     +T ++I GGIRRI  V+  +VP M +GY+  ++++++++   +P    LI
Sbjct: 179 HTVLGGVLTALTLVIIFGGIRRIAHVSSIIVPVMALGYVGLALVIVLLNITHLPEVISLI 238

Query: 246 FTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIG 305
            +HAF    A GG  G A+M     G+ RG+FSNEAG+G+A  A A       V+ GLI 
Sbjct: 239 ISHAFGWEQALGGGVGMALMQ----GIKRGLFSNEAGMGSAPNAAATANVTHPVKQGLIQ 294

Query: 306 MLGTFIDTLIICSLTGLAIITSGVWTSGAS-GAALSSAAFEAAMPGVGHYILSLALVVFA 364
            L  F DTL+ C+ T   I+ SG    G+S G  L+  A    +   G   +++AL  FA
Sbjct: 295 TLAVFTDTLLNCTCTAFIILFSGAPLDGSSNGVQLTQQALTNEIGASGSIFVAVALFFFA 354

Query: 365 YTTILGWSYYGERCWEYLAGTRAIL-PFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAI 423
           +++ILG  YYGE    ++   + +L  +RI+ +  + FG++  LD  W +AD   ALMA+
Sbjct: 355 FSSILGNYYYGEANIRFITAKKWVLHTYRILVSGMVLFGSVATLDLVWSLADITMALMAV 414

Query: 424 PNLIALLLLSPVVFRLTREYFAKARS 449
            NLIA++ L     RL  +Y A+ ++
Sbjct: 415 CNLIAIIFLGKYAIRLLSDYRAQKKA 440


Lambda     K      H
   0.326    0.140    0.437 

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: 496
Number of extensions: 28
Number of successful extensions: 6
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: 449
Length of database: 462
Length adjustment: 33
Effective length of query: 416
Effective length of database: 429
Effective search space:   178464
Effective search space used:   178464
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