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) >FitnessBrowser__Marino:GFF878 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.
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:
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