Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate
Query= TCDB::K7VV21 (488 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639 Length = 464 Score = 294 bits (752), Expect = 5e-84 Identities = 161/434 (37%), Positives = 255/434 (58%), Gaps = 18/434 (4%) Query: 4 SSNSTTEMQVKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVY 63 SS+ ++ +++GLK RHV+M+++ G IG GLF+ SG I AGP L AY GA+V Sbjct: 2 SSSQSSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGP-AVLLAYAAAGALVV 60 Query: 64 FLMTSLGEMATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKF 123 +M LGEMA P +GSFS Y R + GF +GW YW W + + ++ A A + Sbjct: 61 LVMRMLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHA 120 Query: 124 WLPDVPSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMG 183 W P+V W F+L+ +++ + N SVK +GE E+W + +K+ ++ F+ +G L+IFG + Sbjct: 121 WFPNVAIWAFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFL- 179 Query: 184 GHIDVAKNLSVGNHGFVGGLGSFTTG-GGILGVLLVAGFSFQGTELLGITAGEAENPEKS 242 +S +H F G G G +LG +L FSF GTE++ I A E++NP + Sbjct: 180 ----PTSQVSGVSHLF-DTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQ 234 Query: 243 IPKAMNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASI 302 I KA NS+ WRI +FY++SIF++ A++P+ DP L A+ + V ER+G A I Sbjct: 235 ISKATNSVIWRIGLFYLVSIFIVVALVPWNDPIL-----ASVGSYQTVLERMGIPNAKLI 289 Query: 303 MNAVVLTSVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVALL- 361 ++ VVL +V S NS +Y ++RM++SL K G AP + +T+ +G P+ A++ +TA A L Sbjct: 290 VDIVVLVAVTSCLNSALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLA 349 Query: 362 TFLTSIYGVSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPF 421 F + + F FL+++SG + ++ IAIS R R+ +A+G +K+ + LFP Sbjct: 350 VFANYVAPAAVFEFLLASSGAIALLVYLVIAISQLRMRKQRMARG---EKIAFSMWLFP- 405 Query: 422 GPILALIMTVLVTL 435 G A+I+ ++ L Sbjct: 406 GLTYAVIVFIVAAL 419 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: 541 Number of extensions: 30 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: 488 Length of database: 464 Length adjustment: 33 Effective length of query: 455 Effective length of database: 431 Effective search space: 196105 Effective search space used: 196105 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