Align D-serine/D-alanine/glycine transporter (characterized)
to candidate BWI76_RS04870 BWI76_RS04870 aromatic amino acid transporter AroP
Query= SwissProt::A0A0H2VDI7 (470 letters) >FitnessBrowser__Koxy:BWI76_RS04870 Length = 455 Score = 350 bits (899), Expect = e-101 Identities = 183/441 (41%), Positives = 268/441 (60%), Gaps = 5/441 (1%) Query: 19 LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78 L+R L NRHIQLIA+GGAIGTGLF+GS I AGP II Y I GF+ F +MR +GE++ Sbjct: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVIQNAGPGIILGYAIAGFIAFLIMRQLGEMV 69 Query: 79 LSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLSDWVA 138 + SFS FA G +AG+ +GW YW +V+ MA++ A+ Y QFW+P + WV+ Sbjct: 70 VEEPVAGSFSHFAYKYWGGFAGFASGWNYWVLYVLVAMAELTAVGKYVQFWWPEIPTWVS 129 Query: 139 SLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASFA 198 + I + +NL VK+FGEMEFWFA+IK+VA+V++I+ G ++ F G +A+ Sbjct: 130 AAIFFIAINAINLTNVKVFGEMEFWFAIIKVVAVVAMILFGGWLL---FSGNGGPQATVR 186 Query: 199 HLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRIIM 258 +LW GG+ P G +G I +F+F G+ELVG TAAE +PE+S+P+A N + RI++ Sbjct: 187 NLWEQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRILI 246 Query: 259 FYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFST 318 FYV SL V++S+ PWS V + SPFV +F +G A+ +N VVLT+A S NS V+ Sbjct: 247 FYVGSLAVLLSLLPWSRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYCN 306 Query: 319 SRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMITTV 378 SRMLFGLAQ+G APKA + KR VP + S + V++ Y P M V Sbjct: 307 SRMLFGLAQQGNAPKALMSVDKRGVPVNTILVSALVTALCVLINYFAPESAFGLLMALVV 366 Query: 379 SAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVLVLLTLEDD 438 SA++ W +I +++ +R+ + + + L L W+C+ F VLV++ + Sbjct: 367 SALVIN--WAMISLAHIKFRRAKQQQGVVTRFPALLYPLSNWICLLFMAGVLVIMLMTPG 424 Query: 439 TRQALLVTPLWFIALGLGWLF 459 ++ + P+W LG+G+LF Sbjct: 425 MAISVYLIPVWIAVLGVGYLF 445 Lambda K H 0.329 0.141 0.441 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: 631 Number of extensions: 32 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: 470 Length of database: 455 Length adjustment: 33 Effective length of query: 437 Effective length of database: 422 Effective search space: 184414 Effective search space used: 184414 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