GapMind for catabolism of small carbon sources

 

Alignments for a candidate for agcS in Brucella inopinata BO1

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate WP_008510473.1 BIBO1_RS17340 sodium:alanine symporter family protein

Query= TCDB::W0WFC6
         (449 letters)



>NCBI__GCF_000182725.1:WP_008510473.1
          Length = 477

 Score =  300 bits (769), Expect = 5e-86
 Identities = 174/445 (39%), Positives = 261/445 (58%), Gaps = 12/445 (2%)

Query: 11  LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70
           LN V W  +++  +L  G +  + LKF+  V     FR+++    +D+     ISPFQAL
Sbjct: 8   LNNVFWNYILVYGLLAVGFFFTIRLKFVQFVHFPELFRVVFAAGRRDEAG---ISPFQAL 64

Query: 71  MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130
              +A+ VGTGNI GVA A++LGGPGA+FWMW  ALVG+AT +SE  LA  Y+ +++  +
Sbjct: 65  TISIASRVGTGNITGVAVALYLGGPGAIFWMWIVALVGLATAYSESALAQLYKIRNQDGQ 124

Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEVSFGVPDWVTG 190
           + GGP + I  GLG  WA  GA F++   L+   + N VQ N++AD++ ++F +P   TG
Sbjct: 125 YRGGPAFYIARGLGLPWA--GALFSVCLILSFGLVFNAVQANAIADSMVMAFNMPKLGTG 182

Query: 191 VATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHAF 250
           +   +++G+VI GGIR+I +VAE +VPFM   YI+ ++ +L ++ +A+P    LIF+ AF
Sbjct: 183 IVLAILSGVVIFGGIRQIARVAEVVVPFMAFAYILMAICILAINFQAVPSTIALIFSSAF 242

Query: 251 TPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGT--THSAVRSGLIGMLG 308
               A GG  G  + AA+  GV RG+FSNEAG+G+A    A  T   H     G +  LG
Sbjct: 243 GLHEAVGGVTG-GITAAMLNGVKRGLFSNEAGMGSAPNIAAVATPAPHHPSSQGFVQSLG 301

Query: 309 TFIDTLIICSLTGLAIITSGVWT--SGASGAALSSAAFEAAMPGVGHYILSLALVVFAYT 366
            FIDT+++C+ T + I+ SG+    SG +G  L+  A    +  VG Y ++ A+  FA+T
Sbjct: 302 VFIDTILVCTATAIMILLSGILEPGSGLTGTQLTQMAMTHHIGDVGVYFIAAAIFFFAFT 361

Query: 367 TILGWSYYGERCWEY--LAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIP 424
           +I+G   Y E    +  L G   I   R      + +GA   +   +  AD    LMA  
Sbjct: 362 SIIGNYSYAESAMTFLGLGGKVPITILRCALLAMVVWGAYESIHTVFDAADASMGLMATI 421

Query: 425 NLIALLLLSPVVFRLTREYFAKARS 449
           NLIA++LLS  V +LT +YFA+ R+
Sbjct: 422 NLIAIVLLSGTVKKLTVDYFAQRRA 446


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: 558
Number of extensions: 37
Number of successful extensions: 7
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: 477
Length adjustment: 33
Effective length of query: 416
Effective length of database: 444
Effective search space:   184704
Effective search space used:   184704
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 24 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