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 GFF3450 Psest_3515 Na+-dependent transporters of the SNF family
Query= TCDB::Q8NRL8 (579 letters) >FitnessBrowser__psRCH2:GFF3450 Length = 469 Score = 207 bits (528), Expect = 6e-58 Identities = 147/431 (34%), Positives = 214/431 (49%), Gaps = 42/431 (9%) Query: 29 QKGERREVFSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGIPLL 88 Q R ++SSR VF LAA GSAVGLGNIW+FPYV NGGGAF++ Y +L GIPLL Sbjct: 20 QDNASRGLWSSRWVFFLAATGSAVGLGNIWKFPYVTGQNGGGAFVLVYLACILLIGIPLL 79 Query: 89 FLDFAIGHRYRGSAPLAFRRFKKQT------ETIGWIQVGIAFFITIYYAAIIGWAGLYA 142 + IG R R + A R ++ +GW+ F I +Y + GWA Y Sbjct: 80 MTEVMIGRRGRANPDGAVARLAREAGASSRWRVVGWLGGLTGFLILSFYLVVAGWALAYV 139 Query: 143 FKSLNKAWGADPDTYFFSDFLNFDSEA------VVSMDIVPQIAIALFIVWIAAIVVLAI 196 P T F F EA + D + ++ + +V A ++++ Sbjct: 140 -----------PAT-FSGGFAGVSGEASGELFGALLADPL-RLVVCATLVLAATMLIVGF 186 Query: 197 GVDKGIGRVSMVFMPLLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYG 256 GV G+ R MP L ++ L++V+ A + L LF P++ AL +V I A G Sbjct: 187 GVRGGLERSLRFLMPGLFVLMLVLVVYAAIEGEFAQALQFLFVPDFSALTAQSVLI-ALG 245 Query: 257 QIFFSLSVGFGIMLTYSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAG 316 FF+LS+G G M+ Y SYL T++ T ++ A+++ +LAG+ +F + G Sbjct: 246 HAFFTLSLGCGAMMVYGSYLPEGTSIAKTSILVALADTAVALLAGLAIFPLV------FG 299 Query: 317 VGVDEVATSGIGLAFVAFPAIINEMPLGGLFGFLFFSSLTIAGFTSLFSLLEVVVSAVKD 376 G++ A G GL FV P +MPLG + G LFF L IA TS SL E ++ + + Sbjct: 300 NGLEPGA--GPGLIFVTLPIAFGQMPLGQVVGGLFFIMLVIAALTSAISLSEPSIAWLTE 357 Query: 377 KFGLNRKATAIGVGVVMALLSLG-LFSTTS-------GLATLDIMDKFTNNIGIVAVALI 428 +F ++R +G G+V+ LLSLG +FS G D +D T N + L Sbjct: 358 RFRISRTKAVLGSGLVLWLLSLGSVFSFNHWADYQLFGKTFFDTLDYLTTNWLMPLGGLG 417 Query: 429 AVVSIDWVLRR 439 V+ WVL+R Sbjct: 418 TVLFTGWVLQR 428 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: 651 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: 579 Length of database: 469 Length adjustment: 35 Effective length of query: 544 Effective length of database: 434 Effective search space: 236096 Effective search space used: 236096 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