GapMind for catabolism of small carbon sources

 

Aligments for a candidate for metP in Marinobacter adhaerens HP15

Align Transporter, component of The methionine/alanine uptake porter, MetPS (Trotschel et al., 2008) (MetP is the transporter; MetS is an essential auxiliary subunit) (characterized)
to candidate GFF878 HP15_857 sodium-dependent transporter family protein

Query= TCDB::Q8NRL8
         (579 letters)



>lcl|FitnessBrowser__Marino:GFF878 HP15_857 sodium-dependent
           transporter family protein
          Length = 460

 Score =  193 bits (491), Expect = 1e-53
 Identities = 130/437 (29%), Positives = 213/437 (48%), Gaps = 42/437 (9%)

Query: 26  TSPQKGERREVFSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGI 85
           T P + +   ++SSR  FILAA GSAVGLGNIW+FPY+  +NGGGAF++ Y   +   G+
Sbjct: 5   TQPHQ-QANNLWSSRMAFILAAAGSAVGLGNIWKFPYITGENGGGAFVLIYLACIFLIGV 63

Query: 86  PLLFLDFAIGHRYRGSAPLAFRRFKKQTE-------TIGWIQVGIAFFITIYYAAIIGWA 138
           P+L  +  IG R  G +P+A  R   +TE        IGW  V  +F +  +YA I GWA
Sbjct: 64  PVLIAETMIGRR-GGQSPVATMRTLTKTEGTARGWRAIGWNGVIASFLVLSFYAVIGGWA 122

Query: 139 GLYAFKSLNKAW-GADPDTYFFSDFLNFDSEAVVSMDIVPQIAIALFIVWIAAIVVLAIG 197
            +Y  K+    + GAD +         F        +++   ++ + IV    + ++  G
Sbjct: 123 LVYIGKAATGLFTGADAEAIGG----QFGGLLANPWELLMWHSVFMVIV----VFIVGRG 174

Query: 198 VDKGIGRVSMVFMPLLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYGQ 257
           +  G+ +   + MPLL ++ + +VI A+        +  +F+P++  L    V + A G 
Sbjct: 175 IRSGLEKAVNMLMPLLFVLLVAMVIYAMNSGSFGRAVSFMFSPDFSKLTTAGV-LTALGH 233

Query: 258 IFFSLSVGFGIMLTYSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAGV 317
             F+LS+G G+++ Y SYL    N+  T +     ++S  +LAG+ +F  +       G 
Sbjct: 234 AAFTLSIGIGVLMAYGSYLPKTVNIARTAMTIAVVDTSVALLAGLAIFPLVFANGLEPG- 292

Query: 318 GVDEVATSGIGLAFVAFPAIINEMPLGGLFGFLFFSSLTIAGFTSLFSLLEVVVSAVKDK 377
                  +G GL FV  P    +M  G LFG +FF+ L +A  TS  S+LE VV  +++ 
Sbjct: 293 -------AGPGLIFVTLPLAFGQMSGGALFGTIFFALLLVAAITSAISMLEPVVEWLEEH 345

Query: 378 FGLNRKATAIGVGVVMALLS---------------LGLFSTTSGLATLDIMDKFTNNIGI 422
            G++R  +AIG G+ +  +                LG      G    D++D   +N+ +
Sbjct: 346 KGVSRAKSAIGGGLAIWFIGIGTVLSFNVWESVHPLGFIPFFEGKTVFDLLDFLVSNLMM 405

Query: 423 VAVALIAVVSIDWVLRR 439
               L   +   W ++R
Sbjct: 406 PLGGLAIALFAGWAMKR 422


Lambda     K      H
   0.325    0.141    0.430 

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: 663
Number of extensions: 43
Number of successful extensions: 5
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: 579
Length of database: 460
Length adjustment: 35
Effective length of query: 544
Effective length of database: 425
Effective search space:   231200
Effective search space used:   231200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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