Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate AO353_12005 AO353_12005 GABA permease
Query= TCDB::K7VV21 (488 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12005 Length = 463 Score = 295 bits (755), Expect = 2e-84 Identities = 159/431 (36%), Positives = 252/431 (58%), Gaps = 20/431 (4%) Query: 13 VKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGEM 72 +++GLK RHV+M+++ G IG GLF+ SG I AGP L AY G +V +M LGEM Sbjct: 10 LEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGP-AVLLAYAAAGMLVVLVMRMLGEM 68 Query: 73 ATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSWI 132 A P +GSFS Y R + GF +GW YW W + + ++ A A + W P+V W Sbjct: 69 AVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNVAIWA 128 Query: 133 FSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMGGHIDVAKNL 192 F+LI +++ N SVK +GE E+W + IK+ ++ F+++G ++IFG + G + Sbjct: 129 FTLIITLLLTVTNLFSVKNYGEFEFWFALIKVLAIIGFIVLGVMAIFGFLPGSQVSGVSH 188 Query: 193 SVGNHGFV-GGLGSFTTGGGILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAMNSIF 251 GF+ G+G+ +LG +L FSF GTE++ I A E++NP + I KA NS+ Sbjct: 189 LFDTQGFLPNGMGA------VLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVI 242 Query: 252 WRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVVLTSV 311 WRI +FY++SIF++ A++P+ DP L A+ + V ER+G A I++ VVL +V Sbjct: 243 WRIGLFYLVSIFIVVALVPWNDPVL-----ASVGSYQTVLERMGIPNAKLIVDLVVLVAV 297 Query: 312 VSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIA-LLATTAVALLTFLTSIYGV 370 S NS +Y ++RM++SL K G AP + +T+K+G P+ A +L+T A L F + Sbjct: 298 TSCLNSALYTASRMMFSLGKRGDAPAVSQRTNKSGTPYWAVMLSTCAAFLAVFANYVAPA 357 Query: 371 SFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFP---FGPILAL 427 + F FL+++SG + ++ IAIS R R+ +A+G +K+ + LFP + I+ + Sbjct: 358 AVFEFLLASSGAIALLVYLVIAISQLRMRKQRMARG---EKIAFSMWLFPGLTYAVIVFI 414 Query: 428 IMTVLVTLGQD 438 + + + L QD Sbjct: 415 VAALTIMLFQD 425 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: 532 Number of extensions: 25 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: 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