GapMind for catabolism of small carbon sources

 

Alignments for a candidate for agcS in Shewanella loihica PV-4

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 5208581 Shew_1092 amino acid carrier protein (RefSeq)

Query= TCDB::W0WFC6
         (449 letters)



>FitnessBrowser__PV4:5208581
          Length = 492

 Score =  282 bits (722), Expect = 1e-80
 Identities = 163/439 (37%), Positives = 252/439 (57%), Gaps = 18/439 (4%)

Query: 11  LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70
           +NG++WG +++ +++  G+   L L F+ L   G G +L+ QGR K    +  IS FQ  
Sbjct: 16  VNGMLWGSVLIYVLVAAGVLFTLRLGFIQLRMFGHGSKLVLQGREK----TNGISSFQVF 71

Query: 71  MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130
            T +AA VGTGN+AGVA AI +GG GA+FWMW  AL+GMAT F E  LA  Y+ KD   +
Sbjct: 72  CTSMAARVGTGNMAGVAVAITVGGAGAVFWMWLIALLGMATAFIESTLAQVYKVKDSDGQ 131

Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGLA-GFGIGNMVQVNSMADALEVSFGVPDWVT 189
           + GGP Y ++ GLGKR  W+G+ F++   +A GF   N  Q N+M DAL  +FG+   + 
Sbjct: 132 YRGGPAYYMEQGLGKR--WMGSLFSVLLIIAFGFAF-NAAQANTMTDALNNAFGLDKTMV 188

Query: 190 GVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHA 249
           G+  + V   +I GG++++ K +E +VP M V Y+  ++IVLV++ E +P A   I   A
Sbjct: 189 GLVIVAVAAYIISGGLKKVAKASELIVPVMAVAYLAIALIVLVMNLEQVPAALAYIVKSA 248

Query: 250 FTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAG--IAQAAGTTHSAVRSGLIGML 307
           F    A GG      M A+  G+ARG+FSNEAG+G+A    A A+   +     G + M+
Sbjct: 249 FGWEEAAGG-----AMGAMMAGIARGLFSNEAGMGSAANIAASASPNPNHPASQGFVQMI 303

Query: 308 GTFIDTLIICSLTGLAIITSGVWTSGA--SGAALSSAAFEAAMPGVGHYILSLALVVFAY 365
           G F+DT++ICS T   I+ SGV  +     G  L   A    + G   Y ++ A+++F +
Sbjct: 304 GVFVDTIVICSATAAIILLSGVLDAPGEQKGIGLLQLALTNEVGGWAAYFVAFAIILFCF 363

Query: 366 TTILGWSYYGERCWEYLAGTRAIL-PFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIP 424
           ++I+    Y E    +L+ ++ +L  FR +    +  G++  L   W  AD    LMA+ 
Sbjct: 364 SSIIANYSYAESNIMFLSRSKKVLYIFRALVLAMVMAGSVASLQLVWNFADVSMGLMALV 423

Query: 425 NLIALLLLSPVVFRLTREY 443
           N+ A+++LS V F + ++Y
Sbjct: 424 NIAAIVMLSKVAFAVIKDY 442


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: 508
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: 492
Length adjustment: 33
Effective length of query: 416
Effective length of database: 459
Effective search space:   190944
Effective search space used:   190944
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