Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= TCDB::K7VV21 (488 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 304 bits (779), Expect = 4e-87 Identities = 173/457 (37%), Positives = 263/457 (57%), Gaps = 40/457 (8%) Query: 9 TEMQVKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTS 68 T ++RGL+ RH+ ++ALG IG GLFL S + I AGP L +Y+L G ++ +M + Sbjct: 3 TNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGP-AILLSYLLGGVAIFIIMRA 61 Query: 69 LGEMATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDV 128 LGEMA P +GSFS Y Y+ P G+ GWNYW W +T ++TAV + + W PDV Sbjct: 62 LGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDV 121 Query: 129 PSWIFSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLI-IGFLSIFGIMGGHID 187 P WI++L AL+ + ++N +VK +GE E+W + IK+ +VL ++ G + +FG+ Sbjct: 122 PQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGL------ 175 Query: 188 VAKNLSVGNHGFVGGLGSFTTGG--------GILGVLLVAGFSFQGTELLGITAGEAENP 239 GN G G+ + T G G+L L + F++ G E++G+TAGEA+NP Sbjct: 176 -------GNQGVPTGISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNP 228 Query: 240 EKSIPKAMNSIFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIA 299 +KSIP A+NS+FWRIL+FY+ ++FV+ +I P+ + G SPF + FER+G A Sbjct: 229 KKSIPDAINSVFWRILIFYVGALFVIMSIYPWNELGTHG------SPFVMTFERLGIKSA 282 Query: 300 ASIMNAVVLTSVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVA 359 A I+N VVLT+ +S+ N G+Y++ RML++LA+ G AP F+ TS +GIP A+L + VA Sbjct: 283 AGIINFVVLTAALSSCNGGIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVL-VSLVA 341 Query: 360 LL--TFLTSIYGVSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAK 417 LL L + F ++ SA+ W + I+ ++RR + +L + Sbjct: 342 LLFGVLLNYLVPAKVFVWVTSAATFGAIWTWGIVLITQMKYRRGLSEAQR--SQLVFRMP 399 Query: 418 LFPFGPILALIMTVLVT--LGQDP----MLLFGKTWV 448 FP+ LAL VLV +G P L+ G W+ Sbjct: 400 FFPYASYLALAFLVLVVGLMGYFPDTRVALIVGPLWL 436 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: 589 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 488 Length of database: 454 Length adjustment: 33 Effective length of query: 455 Effective length of database: 421 Effective search space: 191555 Effective search space used: 191555 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