GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alsT in Shewanella sp. ANA-3

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 7026278 Shewana3_3420 amino acid carrier protein (RefSeq)

Query= TCDB::W0WFC6
         (449 letters)



>FitnessBrowser__ANA3:7026278
          Length = 452

 Score =  455 bits (1170), Expect = e-132
 Identities = 230/449 (51%), Positives = 308/449 (68%), Gaps = 8/449 (1%)

Query: 3   SLQKWVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSG 62
           S Q  +  LNG+VWGP+ L L++GTG+YL L L+ + + RL +   LL+    K  +  G
Sbjct: 2   SFQALLSSLNGIVWGPVTLCLLVGTGIYLTLRLRLIQVFRLPMALGLLF----KPAKGHG 57

Query: 63  EISPFQALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHY 122
           ++S F AL T L+AT+GTGNI GVATAI +GGPGALFWMW  A  GMATK++E +LAV Y
Sbjct: 58  DLSSFAALCTALSATIGTGNIVGVATAIKMGGPGALFWMWLAAFFGMATKYAECMLAVKY 117

Query: 123 REKDERNEHVGGPMYAIKNGLGKRWAWLGAAFALFG-GLAGFGIGNMVQVNSMADALEVS 181
           R  D R +  GGPMY I+ GLG  W  +   FALFG G+A FGIG   QVN+++DAL ++
Sbjct: 118 RTTDARGQIAGGPMYYIERGLGLHW--MAKLFALFGVGVAFFGIGTFAQVNAISDALTIA 175

Query: 182 FGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGA 241
           F VP W T +   L+   V LGG++RI  VA+ LVP M +GY++A V +LV  AE+I  A
Sbjct: 176 FEVPTWATALVLTLLVAAVTLGGVKRISNVAQKLVPAMSIGYVLACVWILVSFAESILPA 235

Query: 242 FQLIFTHAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRS 301
            QL+   AFTP++A GGF GA V  AI+ G+ARG+FSNE+GLG+A IA AA  T+  V  
Sbjct: 236 LQLVVESAFTPVSAAGGFLGATVAQAIQMGIARGVFSNESGLGSAPIAAAAAKTNEPVEQ 295

Query: 302 GLIGMLGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFE-AAMPGVGHYILSLAL 360
           GL+ M GTF DT+IIC++TGL +I +GVW+   +GAA++SAAF       +G Y++++AL
Sbjct: 296 GLVSMTGTFFDTIIICTITGLVLIITGVWSGDTAGAAMTSAAFSLGGSAAIGQYLVTIAL 355

Query: 361 VVFAYTTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNAL 420
           V FA+TTILGW YYGERCW YL G R +  +++++   I  GA  +LD  WL+ADT+N L
Sbjct: 356 VCFAFTTILGWHYYGERCWYYLVGERGLRAYQMLFLGLIAVGAFIKLDVIWLLADTVNGL 415

Query: 421 MAIPNLIALLLLSPVVFRLTREYFAKARS 449
           MAIPNLIA++ L  V+   T+ YF +  S
Sbjct: 416 MAIPNLIAIIGLRHVIIAETQSYFVRTLS 444


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: 602
Number of extensions: 28
Number of successful extensions: 4
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