Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate GFF295 PS417_01505 gamma-aminobutyrate transporter
Query= TCDB::K7VV21 (488 letters) >FitnessBrowser__WCS417:GFF295 Length = 463 Score = 291 bits (745), Expect = 3e-83 Identities = 160/433 (36%), Positives = 251/433 (57%), Gaps = 18/433 (4%) Query: 5 SNSTTEMQVKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYF 64 S++ + +++GLK RHV+M+++ G IG GLF+ SG I AGP L AY G +V Sbjct: 2 SSTQSSNDLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGP-AVLLAYAAAGTLVVL 60 Query: 65 LMTSLGEMATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFW 124 +M L EMA P +GSFS Y R + GF +GW YW W + + ++ A A + W Sbjct: 61 VMRMLAEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAW 120 Query: 125 LPDVPSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMGG 184 PD+ W+F+L+ +++ + N SVK +GE E+W + IK+ +V F+I+G +IFG + Sbjct: 121 FPDIAIWVFTLVITLLLTATNLFSVKNYGEFEFWFALIKVVAIVGFVILGLAAIFGFL-- 178 Query: 185 HIDVAKNLSVGNHGFVGGLGSFTTG-GGILGVLLVAGFSFQGTELLGITAGEAENPEKSI 243 +S +H F G G G +L +L FSF GTE++ I A E++NP + I Sbjct: 179 ---PTSQVSGVSHLF-DTQGFMPNGMGAVLAAILTTMFSFMGTEIVTIAAAESKNPGQQI 234 Query: 244 PKAMNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIM 303 KA NS+ WRI +FY+LSIF++ +++P+ DP L AA + V ER+G A I+ Sbjct: 235 TKATNSVIWRIGLFYLLSIFIVVSLVPWNDPTL-----AAVGSYQTVLERMGIPNAKLIV 289 Query: 304 NAVVLTSVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVALL-T 362 + VVL +V S NS +Y ++RML+SL + G AP + +T+K+G P+ A+L +T A L Sbjct: 290 DLVVLVAVTSCLNSALYTASRMLFSLGRRGDAPAVAKRTNKSGTPYWAVLLSTGAAFLAV 349 Query: 363 FLTSIYGVSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPFG 422 F + + F FL+++SG + ++ IA+S R R+ A G +K+ + LFP G Sbjct: 350 FANYVAPAAVFEFLLASSGAIALLVYLVIAVSQLRMRQKRTAAG---EKIVFKMWLFP-G 405 Query: 423 PILALIMTVLVTL 435 A+++ ++ TL Sbjct: 406 LTYAVMVFIVGTL 418 Lambda K H 0.326 0.141 0.425 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: 530 Number of extensions: 30 Number of successful extensions: 7 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: 488 Length of database: 463 Length adjustment: 33 Effective length of query: 455 Effective length of database: 430 Effective search space: 195650 Effective search space used: 195650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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