Aligments for a candidate for agcS in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for agcS in Shewanella amazonensis SB2B

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 6938850 Sama_2953 sodium:alanine symporter family protein (RefSeq)

Query= TCDB::W0WFC6
         (449 letters)



>lcl|FitnessBrowser__SB2B:6938850 Sama_2953 sodium:alanine symporter
           family protein (RefSeq)
          Length = 464

 Score =  447 bits (1151), Expect = e-130
 Identities = 231/439 (52%), Positives = 302/439 (68%), Gaps = 8/439 (1%)

Query: 8   VVDLNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPF 67
           +  LN +VWGP+ L L++GTG+Y  + LK + LV+L +   LL++  S      GE+S F
Sbjct: 7   LTQLNAIVWGPVTLCLLVGTGVYFTVRLKLLQLVKLPLALSLLFKPAS----GKGELSSF 62

Query: 68  QALMTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDE 127
            AL T L+AT+GTGNI GVATAI LGGPGALFWMW  A  GMATK++E +LA+ YR  D 
Sbjct: 63  GALCTALSATIGTGNIVGVATAIKLGGPGALFWMWVAAFFGMATKYAECLLALKYRTTDA 122

Query: 128 RNEHVGGPMYAIKNGLGKRWAWLGAAFALFG-GLAGFGIGNMVQVNSMADALEVSFGVPD 186
           R    GGPMY I+ GLG    WL   FA+FG G+A FGIG   QVN+++DA+ V+F VP 
Sbjct: 123 RGNIAGGPMYYIERGLGL--GWLARLFAIFGVGVAFFGIGTFAQVNAISDAMTVAFAVPT 180

Query: 187 WVTGVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIF 246
           WVT     L+   V LGG++RI  VA+ LVP M +GY++A + VL+   +AI  A  L+ 
Sbjct: 181 WVTASVLTLLVAAVTLGGVKRIASVAQTLVPAMAIGYVLACLWVLLSLHDAIVPALSLVV 240

Query: 247 THAFTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGM 306
             AFTP+AA GGF GA V  AI+ G+ARG+FSNE+GLG+A IA A   T   V  GL+ M
Sbjct: 241 NGAFTPVAAGGGFLGATVALAIQTGIARGVFSNESGLGSAPIAAATARTKEPVEQGLVSM 300

Query: 307 LGTFIDTLIICSLTGLAIITSGVWTSGASGAALSSAAFEAAM-PGVGHYILSLALVVFAY 365
            GTF DTLIIC++TGL +I +GVW+  ++GAA++SAAF AA  P +G Y++++ALV FA+
Sbjct: 301 TGTFFDTLIICTMTGLVLIITGVWSGDSAGAAMTSAAFSAATNPLLGQYLVTVALVCFAF 360

Query: 366 TTILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPN 425
           TTILGW+YYGERCW YL G R    +R+V+ L I  GA  +LD  WL+AD +N LMAIPN
Sbjct: 361 TTILGWNYYGERCWSYLTGGRYAGLYRLVFLLLIAGGAFIKLDLIWLLADIVNGLMAIPN 420

Query: 426 LIALLLLSPVVFRLTREYF 444
           LIAL+ L  V+   ++ YF
Sbjct: 421 LIALIGLRSVILAESQRYF 439


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: 660
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: 464
Length adjustment: 33
Effective length of query: 416
Effective length of database: 431
Effective search space:   179296
Effective search space used:   179296
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:

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