Align L-alanine and D-alanine permease (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05965 Length = 466 Score = 407 bits (1046), Expect = e-118 Identities = 207/462 (44%), Positives = 295/462 (63%), Gaps = 15/462 (3%) Query: 11 ETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIM 70 E Q G LKR L RHI+L+ALG IG GLFLGSA ++ AGP+++L Y I G +IM Sbjct: 4 EQLQQGVLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIM 63 Query: 71 RALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFP 130 R LGEM V PVAGSFS +A +Y G AGFL+GWNYW L+++ +AE+TAV Y+ W+P Sbjct: 64 RQLGEMIVEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWP 123 Query: 131 DVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDG 190 +VP W+ A V + IN + VK FGE EFWFA+IK+V II M+ G ++ G G G Sbjct: 124 EVPTWVSAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTG--G 181 Query: 191 VALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 250 +SNLW+HGGF PNG +G+LM++ +MF++ G+E++G+TA EA P+K IP AI V Sbjct: 182 PQASVSNLWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQV 241 Query: 251 FWRILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFVV 301 +R+L+FYVGAL V+LS+YPW+++ GSPFV F +G TAA I+NFVV Sbjct: 242 VYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVV 301 Query: 302 ITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNY 361 +TAALS N G++ RMLY LA+ G AP K + GVP RAL +S +L V++NY Sbjct: 302 LTAALSVYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNY 361 Query: 362 LVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALK-YRMWLYPVSSYLAL 420 + P + + ++ + W MI L LKFRK++ +R + ++ + P ++YL L Sbjct: 362 VAPNEALELLFALVVASLMINWAMISLTHLKFRKAM--GQRGIVPGFKAFWSPYTNYLCL 419 Query: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYTFKLQPT 462 AF+ +++ +M P R ++Y P ++++L V FY ++ T Sbjct: 420 AFMAMIIYVMLLIPGVRASVYAIPVWVLILFV-FYRIRVART 460 Lambda K H 0.328 0.142 0.444 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: 666 Number of extensions: 35 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: 473 Length of database: 466 Length adjustment: 33 Effective length of query: 440 Effective length of database: 433 Effective search space: 190520 Effective search space used: 190520 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 (21.7 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