GapMind for catabolism of small carbon sources

 

Alignments for a candidate for agcS in Desulfovibrio vulgaris Hildenborough

Align Probable Glycine/alanine/asparagine/glutamine uptake porter, AgcS (characterized)
to candidate 206150 DVU0724 sodium/alanine symporter family protein

Query= TCDB::W0WFC6
         (449 letters)



>MicrobesOnline__882:206150
          Length = 468

 Score =  434 bits (1115), Expect = e-126
 Identities = 228/437 (52%), Positives = 294/437 (67%), Gaps = 6/437 (1%)

Query: 11  LNGVVWGPLMLVLILGTGLYLMLGLKFMPLVRLGVGFRLLWQGRSKDDESSGEISPFQAL 70
           +N  VWGP +L L++GTG+YL + L  + +VRL +  R ++ GR  +    G++S F AL
Sbjct: 10  VNAFVWGPPLLALLVGTGIYLTIRLGLLQVVRLPLALRYVF-GRDDEHHEEGDVSSFAAL 68

Query: 71  MTCLAATVGTGNIAGVATAIFLGGPGALFWMWCTALVGMATKFSEVVLAVHYREKDERNE 130
            T LAAT+GTGNI GVATA+  GGPGALFWMW  A  GMATK++E +LAV YR  D   +
Sbjct: 69  CTALAATIGTGNIVGVATAVAAGGPGALFWMWVAAFFGMATKYAEGLLAVKYRVTDANGQ 128

Query: 131 HVGGPMYAIKNGLGKRWAWLGAAFALFGGL-AGFGIGNMVQVNSMADALEVSFGVPDWVT 189
             GGPMY ++ GLG R   L  AFAL G L A FGIG   QVN++ DA  +S G+P   T
Sbjct: 129 MSGGPMYYLERGLGSRM--LARAFALCGILVAFFGIGTFAQVNAIKDAASLSLGIPPLAT 186

Query: 190 GVATMLVTGLVILGGIRRIGKVAEALVPFMCVGYIVASVIVLVVHAEAIPGAFQLIFTHA 249
            V       LV LGG+R I +VAE +VPFM V YI+AS  VLV+H + IP A  +I   A
Sbjct: 187 AVVLTTTVALVTLGGLRSIARVAEKVVPFMAVFYIIASCAVLVMHLDRIPDAVMVILHSA 246

Query: 250 FTPIAATGGFAGAAVMAAIRFGVARGIFSNEAGLGTAGIAQAAGTTHSAVRSGLIGMLGT 309
           F P AA GG AG  V+ A+R GVARG+FSNE+GLG+A IA AA  T S VR GLI M GT
Sbjct: 247 FNPQAALGGAAGMTVLTAMRAGVARGVFSNESGLGSAPIAAAAARTKSCVRQGLISMTGT 306

Query: 310 FIDTLIICSLTGLAIITSGVWTS-GASGAALSSAAFEAAM-PGVGHYILSLALVVFAYTT 367
           F DT++IC++TGL ++ +GVW     +GAA+++AAF A +   +G Y  +L L++FA+TT
Sbjct: 307 FFDTIVICTMTGLVLVVTGVWNDPQLAGAAMTNAAFAAGLESSLGQYAATLGLILFAFTT 366

Query: 368 ILGWSYYGERCWEYLAGTRAILPFRIVWTLAIPFGAMTQLDFAWLVADTLNALMAIPNLI 427
           ILGW+YYGERC EYL G R ILP+R+V+   +  GA   L+  W++AD +N LMAIPNLI
Sbjct: 367 ILGWNYYGERCTEYLFGVRGILPYRLVFIGLVAAGAFVHLELIWVLADIVNGLMAIPNLI 426

Query: 428 ALLLLSPVVFRLTREYF 444
            LL LS V+   TR +F
Sbjct: 427 GLLGLSGVIIAETRAFF 443


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: 576
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: 468
Length adjustment: 33
Effective length of query: 416
Effective length of database: 435
Effective search space:   180960
Effective search space used:   180960
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