Aligments for a candidate for agcS in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for agcS in Shewanella oneidensis MR-1

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 200044 SO0858 sodium:alanine symporter family protein (NCBI ptt file)

Query= TCDB::W0WFC6
         (449 letters)



>lcl|FitnessBrowser__MR1:200044 SO0858 sodium:alanine symporter
           family protein (NCBI ptt file)
          Length = 452

 Score =  456 bits (1172), Expect = e-133
 Identities = 230/446 (51%), Positives = 307/446 (68%), Gaps = 8/446 (1%)

Query: 3   SLQKWVVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSG 62
           + Q  +  LNG+VWGP+ L L++GTG+YL   LK + + RL +   LL+    K  +  G
Sbjct: 2   NFQALLSSLNGIVWGPITLCLLVGTGVYLTTRLKLIQVFRLPMALSLLF----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 RW  +   FALFG G+A FGIG   QVN+++DAL ++
Sbjct: 118 RTTDARGQIAGGPMYYIERGLGLRW--MAKLFALFGVGVAFFGIGTFAQVNAISDALTIA 175

Query: 182 FGVPDWVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGA 241
           F VP W T +   L+   V LGG++RI  VA+ LVP M +GY++A V +L+  AEAI  A
Sbjct: 176 FDVPTWTTALVLTLLVAAVTLGGVKRISNVAQKLVPAMSIGYVLACVWILLGFAEAILPA 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 GLVSMTGTFFDTIIICTMTGLVLIITGVWSGDTAGAAMTSAAFSLGGSAAIGQYLVTIAL 355

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

Query: 421 MAIPNLIALLLLSPVVFRLTREYFAK 446
           MAIPNLIA++ L  ++   T+ YF +
Sbjct: 416 MAIPNLIAIIGLRHIIIAETQSYFVR 441


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: 619
Number of extensions: 29
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources