GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntT in Pseudomonas fluorescens GW456-L13

Align gluconate:H+ symporter (gntT) (characterized)
to candidate PfGW456L13_3649 D-serine permease DsdX

Query= reanno::Cup4G11:RR42_RS28835
         (453 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3649
          Length = 446

 Score =  365 bits (937), Expect = e-105
 Identities = 190/449 (42%), Positives = 286/449 (63%), Gaps = 5/449 (1%)

Query: 5   TGTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGT 64
           +G TLL+    A+I +V LI K +++ F+ L   S ++G   GMP+  +  S+E GVGGT
Sbjct: 3   SGPTLLVVLFSAIILIVFLIVKVRVHAFLALTAASFVVGIGSGMPLAQMASSYEKGVGGT 62

Query: 65  LGHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVG 124
           LG +A ++GLG +LGKM+ ESGGAERIA+TL+   G++   WAM+ + FI G+PVFFEVG
Sbjct: 63  LGFLATIIGLGGILGKMLEESGGAERIAQTLLSTLGKERASWAMMLVGFIAGIPVFFEVG 122

Query: 125 FVLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTILY 184
           FVLL+P+ + VAK T  +++ +G+P+   L  VH ++PPHPAA+       AD+GK I+Y
Sbjct: 123 FVLLIPLIYVVAKETRINLLYLGVPLAVSLMAVHCMLPPHPAAMAITGLLGADVGKVIVY 182

Query: 185 ALIVGIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITLFTIL 244
            LI+ +PTA IAGPL+ KL+ +    PD       F +E     A+ +LPG G+TL TIL
Sbjct: 183 GLIIALPTAIIAGPLWIKLVCK-SEAPDTQ---EAFLDEHCVDSATRDLPGLGLTLLTIL 238

Query: 245 LPVILMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRENILR 304
           LP++LM+  S+A  +       +  +  +G  +IAL IA + +++  G RRG +  ++L 
Sbjct: 239 LPLLLMVGKSFAAGLPHDSGLFS-IVSFLGTPLIALSIAVVFAYWALGLRRGLSMPDLLA 297

Query: 305 FTNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVLIRIA 364
            T +   P A I L++GAGG F  +L DSG+ NA+    T  +++ ++L WLVA L+  A
Sbjct: 298 HTQKSFPPLASILLIIGAGGAFNGILVDSGVGNALSGSLTQLNMNPIVLAWLVAGLMHFA 357

Query: 365 TGSATVAMTTAAGIVAPIAASVPGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYFNMTV 424
            GSATVAM +AAG+V P+ ++ P    E++ +  GAG++  +HV D  FW+VKEY  +++
Sbjct: 358 VGSATVAMISAAGMVMPMLSAHPTVSKEIICIAIGAGAIGWTHVTDSAFWVVKEYLGVSL 417

Query: 425 AQTFKTWSVCETLISVIALLLTLALATVV 453
           A+  K ++    L S+IAL LTL L+  V
Sbjct: 418 AEALKKFTSATVLASLIALGLTLLLSQFV 446


Lambda     K      H
   0.326    0.141    0.410 

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: 41
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: 453
Length of database: 446
Length adjustment: 33
Effective length of query: 420
Effective length of database: 413
Effective search space:   173460
Effective search space used:   173460
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 (21.6 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