GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alsT in Echinicola vietnamensis KMM 6221, DSM 17526

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate Echvi_4032 Echvi_4032 amino acid carrier protein

Query= TCDB::W0WFC6
         (449 letters)



>FitnessBrowser__Cola:Echvi_4032
          Length = 452

 Score =  325 bits (832), Expect = 2e-93
 Identities = 179/451 (39%), Positives = 259/451 (57%), Gaps = 18/451 (3%)

Query: 8   VVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPF 67
           ++D +  +WG  +L L+LG G  L L    +P    G   +++  G+  D  + G+I+ F
Sbjct: 5   IIDFSNWIWGWPLLYLLLGGGTLLFLYSGLIPFRGFGHAMKVVG-GKYDDPNAKGDITSF 63

Query: 68  QALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDE 127
           QAL + +AATVG GNI+GVA AI  GGPGA+FWMW +A VGMATK+    LA+ YR KD 
Sbjct: 64  QALSSAIAATVGLGNISGVALAIGTGGPGAIFWMWVSAFVGMATKYFTCTLAIMYRGKDS 123

Query: 128 RNEHVGGPMYAIKNGLGKRWAWLGAAFALFGGLAGFGIGNMVQVNSMADALEV----SFG 183
                GGPMY I+ G+GK+W +L   F + G +   G+  + Q N + D + V     FG
Sbjct: 124 SGHIQGGPMYVIEEGMGKKWRFLSVIFCVAGIM---GLLAIFQANQLTDVIRVVLLKPFG 180

Query: 184 VPD-----WVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAI 238
           +       W+ GV+ ML+   VILGGI+RI  VA  LVPFM   Y ++ +++L    + I
Sbjct: 181 LDHGTTTRWILGVSMMLLVATVILGGIQRIAAVASKLVPFMVTLYFISVLVILFRFGDEI 240

Query: 239 PGAFQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSA 298
             +F  I   AFT  A  GG  GA ++     G  R  FSNEAG+GTA +   A      
Sbjct: 241 LPSFWFILEDAFTGKAVLGGSIGAVIIT----GARRAAFSNEAGIGTAPMVHGASKNEEP 296

Query: 299 VRSGLIGMLGTFIDTLIICSLTGLAIITSGVWTSG-ASGAALSSAAFEAAMPGVGHYILS 357
           VR GLI MLG FIDT+++C+LT + I+ +GVW +G   G  ++ +AF++ +P VG Y L 
Sbjct: 297 VREGLIAMLGPFIDTIVVCTLTAMTIMVTGVWETGEKDGVLMTLSAFQSGIPVVGKYFLM 356

Query: 358 LALVVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTL 417
            A++VFA +T+  +SYYG +C+ YL G      +   + L I  GA+  L       D +
Sbjct: 357 AAVLVFALSTMFTYSYYGHKCFNYLFGADKANYYNYFYLLTIVGGAVVSLKVVMSFVDGM 416

Query: 418 NALMAIPNLIALLLLSPVVFRLTREYFAKAR 448
            A+MA P +I+ + LSP V   T++YF + +
Sbjct: 417 YAVMAFPTMISAIYLSPKVRAATKDYFRRMK 447


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: 580
Number of extensions: 28
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: 449
Length of database: 452
Length adjustment: 33
Effective length of query: 416
Effective length of database: 419
Effective search space:   174304
Effective search space used:   174304
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