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 GFF3445 Psest_3510 Na+-dependent transporters of the SNF family
Query= TCDB::Q8NRL8 (579 letters) >FitnessBrowser__psRCH2:GFF3445 Length = 486 Score = 195 bits (496), Expect = 3e-54 Identities = 137/419 (32%), Positives = 212/419 (50%), Gaps = 30/419 (7%) Query: 34 REVFSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGIPLLFLDFA 93 + ++ SR FILAA GSAVGLGNIW+FPY+ + GGGAF++ Y + +L G+P++ + A Sbjct: 7 KNLWLSRWGFILAATGSAVGLGNIWKFPYITGEFGGGAFVLMYLLCILAIGVPVMMCEIA 66 Query: 94 IGHRYRGSAPLAFRRFKKQT------ETIGWIQVGIAFFITIYYAAIIGWAGLYAFKSLN 147 IG R RGS A R ++ + +G + + F I +Y + GWA Y K L+ Sbjct: 67 IGRRGRGSPIDAIGRVVRENNGNPLWKAVGGMAMTAGFLILCFYVVVAGWAFAYTVKMLD 126 Query: 148 KAWGADPDTYFFSDFLNFDSEAVVSMDIVPQIAIALFIVWIAAIVVLAIGVDKGIGRVSM 207 + A F +S + +AL +WI +A GV KGI Sbjct: 127 GSLAATSVEALGGVFEAHNSNPWQLGGW--SLLVALLTLWI-----VAKGVQKGIENAVR 179 Query: 208 VFMPLLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYGQIFFSLSVGFG 267 MP L ++ LI+V AV G + G LF+ + + + +AA G FF+LS+ G Sbjct: 180 WMMPGLAVLLLILVGYAVTSGGFDQGFAFLFSFDTSKITGEAL-LAALGHAFFTLSLASG 238 Query: 268 IMLTYSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAGVGVDEVATSGI 327 +LTY SY+ ++ T + A++ +LAG+ +F + AN G+D T+G Sbjct: 239 AILTYGSYIPDDQSIARTTFMVAIADTCVALLAGLAIFP---IIFAN---GMD--PTAGP 290 Query: 328 GLAFVAFPAIINEMPLGGLFGFLFFSSLTIAGFTSLFSLLEVVVSAVKDKFGLNRKATAI 387 GL F++ P +MP G FG LFF+ ++IA TS S++E V+ + +K G++R A+ Sbjct: 291 GLIFMSLPLAFQQMPFGTAFGVLFFAMVSIAALTSAISMIEATVAYLNEKHGISRLKAAM 350 Query: 388 GVGVV------MALLSLGLFS--TTSGLATLDIMDKFTNNIGIVAVALIAVVSIDWVLR 438 G G V +A+LS L S T G D +D T+ + + V+ + LR Sbjct: 351 GSGAVLLVISMLAMLSFNLMSGWTPMGKNFFDWLDYLTSRWMMPLGGIFTVLLAGYALR 409 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: 688 Number of extensions: 36 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: 486 Length adjustment: 35 Effective length of query: 544 Effective length of database: 451 Effective search space: 245344 Effective search space used: 245344 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