Align DL-alanine permease SerP2 (characterized)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= SwissProt::A2RI86 (460 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 214 bits (545), Expect = 5e-60 Identities = 125/401 (31%), Positives = 208/401 (51%), Gaps = 6/401 (1%) Query: 7 DENIEKQPS-QRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYI 65 D +E++ QRGL + +IAI G IGTGLFLG+G +I GPS++ Y I + + Sbjct: 9 DTIVEREKGLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYAIGALIALL 68 Query: 66 LLRAIGEMLYQDPSQHSFLNFVSRYMGAKPGYFIQWSYLLVVVFVAMAELIAIGTYINFW 125 L+ + EM P+ SF + Y+ G+ ++++Y +VF E+ AI Y+ +W Sbjct: 69 LMGCLAEMTVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYW 128 Query: 126 LPDLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHT 185 P +P W V L +N+++ K FG E+ F M+KIVAI+G IL ++F Sbjct: 129 FPAVPGWYWIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYVVFG--AP 186 Query: 186 GTDTVSLTNITKGFEFFPNGVSSFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAIN 245 T+ N T FFP GV + + + +F+++S+E I + A E +P+ + +A Sbjct: 187 ADSTIGFANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFR 246 Query: 246 QIPIRIVLFYIGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASA 305 R+V FY+ L +++I W D+SPFV + + AA ++NFV+L +A SA Sbjct: 247 ATMFRLVFFYLLTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSA 306 Query: 306 LNSALFSITRNLYSLSQLNDDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPAIS 365 +NS L+ TR ++SLS+ + + GVPV AL +++ I ++++ Sbjct: 307 MNSQLYITTRMMFSLSRAG--YAPRKLGALNGKGVPVAALWLSTIGIALATVLNVVYP-D 363 Query: 366 NSFVFITSVATNLFLVVYLMTLITYLKYRKSKDFDPSGFTL 406 SFV + SV+ + +LM +T+ +R P F + Sbjct: 364 ASFVLMMSVSMFGAMFTWLMIFVTHFFFRHRHQGAPLAFRM 404 Lambda K H 0.330 0.144 0.431 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: 573 Number of extensions: 33 Number of successful extensions: 3 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: 460 Length of database: 466 Length adjustment: 33 Effective length of query: 427 Effective length of database: 433 Effective search space: 184891 Effective search space used: 184891 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 (21.8 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