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 5210455 Shew_2896 sodium:neurotransmitter symporter (RefSeq)
Query= TCDB::Q8NRL8 (579 letters) >FitnessBrowser__PV4:5210455 Length = 503 Score = 379 bits (973), Expect = e-109 Identities = 208/502 (41%), Positives = 302/502 (60%), Gaps = 7/502 (1%) Query: 33 RREVFSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGIPLLFLDF 92 +RE ++SR FILAA+GSA+GLGNIWRFPY+AYDNGGGAF IPY A++TAGIP + ++F Sbjct: 2 KREQWNSRVGFILAAVGSAIGLGNIWRFPYMAYDNGGGAFFIPYLFAMITAGIPFMIMEF 61 Query: 93 AIGHRYRGSAPLAFRRFKK----QTETIGWIQVGIAFFITIYYAAIIGWAGLYAFKSLNK 148 ++GH+ + ++P F + + E +GW QV IA I +YY AIIGW Y S ++ Sbjct: 62 SLGHKIKKTSPRIFAQLGHTLGFRLEWLGWFQVFIAAVIAVYYVAIIGWTLSYLGFSFSQ 121 Query: 149 AWGADPDTYFFSDFLNFDSEAVVSM-DIVPQIAIALFIVWIAAIVVLAIGVDKGIGRVSM 207 AWG +P+ +FF+ +L + + + + IAIA+ I W+ + + GV GI R + Sbjct: 122 AWGDNPNDFFFNHYLKLGNNSPSHLGEFQIGIAIAMSIAWLMTFMAVFTGVKGGIERANK 181 Query: 208 VFMPLLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYGQIFFSLSVGFG 267 + MP+L I+ L+++ + + LPGA GL+ LF P++ L + VW AAYGQIFF+LSVGF Sbjct: 182 IMMPMLFIMVLVLIGRIMFLPGALSGLNYLFEPDFSRLLDAQVWSAAYGQIFFTLSVGFA 241 Query: 268 IMLTYSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAGVGVDEVATSGI 327 IML YSSYL + ++ + +T N F +LAGI +F LG+MA + EV +SGI Sbjct: 242 IMLAYSSYLPTKADINNNAFMTVLINCGFSILAGILIFGVLGYMAEEQMKPLTEVVSSGI 301 Query: 328 GLAFVAFPAIINEMPLGGLFGFLFFSSLTIAGFTSLFSLLEVVVSAVKDKFGLNRKATAI 387 GLAFV P IN MP + G LFF +L IAG +S S++E V SAV DKF + RK A+ Sbjct: 302 GLAFVTIPTAINLMPAPYILGPLFFIALVIAGLSSHISIIEAVTSAVIDKFHVRRKPAAV 361 Query: 388 GVGVVMALLSLGLFSTTSGLATLDIMDKFTNNIGIVAVALIAVVSIDWVLRRIDEFSTHL 447 V + L+S+ F+T GL LD++D F NNI ++ L+ +V I W+L ++ H Sbjct: 362 LVCSLGYLVSMA-FATNGGLLLLDLVDYFINNIALLLSCLLELVIITWLL-KVTVIHQHA 419 Query: 448 NAISAFKVNTIWRISVVNITTLVLGSTLALELTSLINEPYGGYTVLQNGLFGWGVLAVIL 507 N S F+V + + + I+ +L + LA L + + YG Y + GWG++ +L Sbjct: 420 NENSEFRVGGWFVVCLRFISPAILATILAKNLYNTLVNGYGDYPIADQLFLGWGLVGTML 479 Query: 508 VAAFLLPMVSWPKGTLVDGPPG 529 A L+ S G P G Sbjct: 480 FFAVLINFTSKSPGYPDQHPGG 501 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: 711 Number of extensions: 31 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: 579 Length of database: 503 Length adjustment: 35 Effective length of query: 544 Effective length of database: 468 Effective search space: 254592 Effective search space used: 254592 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