Align Leu/Val/Ile amino-acid permease; Branched-chain amino-acid permease 2 (characterized)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= SwissProt::P38084 (609 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 206 bits (525), Expect = 1e-57 Identities = 138/473 (29%), Positives = 230/473 (48%), Gaps = 24/473 (5%) Query: 83 ESITSDSKLKKSMKSRHVVMMSLGTGIGTGLLVANAKGLHYGGPAALIIGYILVSFVTYF 142 + I +LK+ +K+RH+ +++LG IGTGL + +A L GP+ +I+GY + F+ + Sbjct: 3 DEILRQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIAGFIAFL 61 Query: 143 MIQAAGEMAVTYPTLPANFNAYSSIFISKSFGFATVWLYCFQWLTVLPLELITASMTIQF 202 +++ GEM V P + +F+ ++ + GF + W Y ++ V EL +QF Sbjct: 62 IMRQLGEMIVEEP-VAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQF 120 Query: 203 WNDKINPDIYILIFYVFLVFIHFFGVKAYGETEFIFNCCKILMIAGFIILSIVINCGGAG 262 W ++ + +F+V + I+ VK +GE EF F K++ I G I L + G G Sbjct: 121 WWPEVPSWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLFSGTG 180 Query: 263 NDGYIGATYWHNPGAFAGDTSIGRFKNVCYILVTAYFSFGGMELFALSVQEQSNPRKSTP 322 + W + G F S G + +I+ FSFGG+EL ++ E S P K P Sbjct: 181 GPQASVSNLWDHGGFFPNGYS-GLLMAMAFIM----FSFGGLELVGITAAEASEPGKVIP 235 Query: 323 VAAKRSIYRIVVIYLLTMILIGFNVPYNDD-QLMGAGGSATHASPYVLAASIHGVKIVPH 381 A + +YR+++ Y+ + ++ P++ Q +GA G A SP+V S+ G H Sbjct: 236 KAINQVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAH 295 Query: 382 IINAVILISVVSVANSSLYAGPRLICSLAQQGYAPKFLDYVDREGRPLRALIVCCVFGVI 441 I+N V+L + +SV NS +Y R++ LA+QG APK L ++++G PL AL V + ++ Sbjct: 296 ILNFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLL 355 Query: 442 AFVAASSKEEIVFTWLAAIAGLSELFTWTSIMLSHLRFRQAMKVQGRSLDELGYKATTGI 501 + + L A+ S + W I L+HL+FR+ M QG G+K Sbjct: 356 SVLVNYLAPHEALELLFALVVASLMINWAMISLTHLKFRKIMSQQG---IVPGFK----- 407 Query: 502 WGSIYGVFFNILVFVAQFWVALAPLGNGGKCDAESFFQNYLAFPIWLAFYFGY 554 S + F N L + L G + A P+W+ FG+ Sbjct: 408 --SFWFPFSNYLCLAFMVMIVCVMLMIPG------IRASVFAIPVWVLIIFGF 452 Lambda K H 0.325 0.139 0.423 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: 727 Number of extensions: 36 Number of successful extensions: 5 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: 609 Length of database: 467 Length adjustment: 35 Effective length of query: 574 Effective length of database: 432 Effective search space: 247968 Effective search space used: 247968 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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