Align L-alanine and D-alanine permease (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 402 bits (1034), Expect = e-116 Identities = 192/444 (43%), Positives = 290/444 (65%), Gaps = 3/444 (0%) Query: 7 LPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAI 66 +P+ LKR L RHI+L+ALG IG GLFLG A+ I+MAGP+++L Y + G+ Sbjct: 2 VPNASDNTDATLKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIA 61 Query: 67 LVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMG 126 IMR LGEM V PVAGSFS +A Y G AGF++GWNYW L+++ +AE++AV +Y+ Sbjct: 62 FFIMRQLGEMVVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQ 121 Query: 127 IWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGF 186 W+P +P W AL + + +INL +VK+FGE EFWF+++K++ I+ M++ G ++A G Sbjct: 122 YWWPHIPTWASALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGT 181 Query: 187 GNDGVALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNA 246 G +SNLW HGGF PNG+SG++M++ ++MF++ G+E++G+TA EA P+KTIP A Sbjct: 182 A--GPQASVSNLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKA 239 Query: 247 IGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAAL 306 V +RIL+FYVGAL V+LS+YPW ++ T GSPFV+ F + A ++N VV+TAAL Sbjct: 240 TNQVIYRILIFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAAL 299 Query: 307 SSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEK 366 S N G++ RML+ LA+ G AP K + G+P AL +S A V++NY +P + Sbjct: 300 SVYNSGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGE 359 Query: 367 VFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLV 426 F + + I W MI + LKFR+ A+ + +++ YP+++Y+ LAFL + Sbjct: 360 AFELLMGLVVSALIINWAMISIIHLKFRRDKRAAGQET-RFKSLGYPLTNYVCLAFLAGI 418 Query: 427 VGLMAYFPDTRVALYVGPAFLVLL 450 + +M P R+++Y+ PA+L +L Sbjct: 419 LYVMYLTPGLRISVYLIPAWLAVL 442 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: 648 Number of extensions: 42 Number of successful extensions: 2 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: 465 Length adjustment: 33 Effective length of query: 440 Effective length of database: 432 Effective search space: 190080 Effective search space used: 190080 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