Align Leu/Val/Ile amino-acid permease (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= CharProtDB::CH_091448 (609 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 209 bits (532), Expect = 2e-58 Identities = 132/402 (32%), Positives = 217/402 (53%), Gaps = 16/402 (3%) Query: 91 LKKSMKSRHVVMMSLGTGIGTGLLVANAKGLHYGGPAALIIGYILVSFETYFMIQAAGEM 150 LK+ +K+RH+ +++LG IGTGL + +A L GP+ +I+GY + F + +++ GEM Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIAGFIAFLIMRQLGEM 69 Query: 151 AVTYPTLPANFNAYSSIFISKSFGFATVWLYCFQWLTVLPLELITASMTIQFGNDKINPD 210 V P + +F+ ++ + GF W Y ++ V EL IQF I Sbjct: 70 IVEEP-VAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTW 128 Query: 211 IYILIFYVFLVFIHFFGVKAYGETEFIFNCCKILMIAGFIILSIVINCGGAGNDGYIGAT 270 + L+F+V + I+ VK +GETEF F K++ I G I+L + G G + Sbjct: 129 VSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGPQASVSN 188 Query: 271 YWHNPGAFAGDTSIGRFKNVCYILVTAYFSFGGMELFALSVQEQSNPRKSTPVAAKRSIY 330 W + G F + +G ++ +I+ FSFGG+EL ++ E S PRK P A + +Y Sbjct: 189 LWSH-GGFFPNGGMGLLMSMAFIM----FSFGGLELVGITAAEASEPRKVIPKAINQVVY 243 Query: 331 RIVVIYLLTMILIGFNVPYNDD-QLMGAGGSATHASPYVLAASIHGVKIVPHIINAVILI 389 RI++ Y+ + ++ P++ Q +GA G A SP+V S+ G HI+N V+L Sbjct: 244 RILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLT 303 Query: 390 SVVSVANSSLYAGPRLICSLAQQGYAPKFLDYVDREGRPLRAL----IVCCVFGVIAFVA 445 + +SV NS +Y R++ LA+QG APK L ++++G P+RAL +V + V+ +VA Sbjct: 304 AALSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVA 363 Query: 446 ASSKEEIVFTWLAAIAGLSELFTWTSIMLSHLRFRQAMKVQG 487 S E++F + A S + W I ++H++FR+AM QG Sbjct: 364 PQSALELLFALVVA----SLMINWALISITHIKFRKAMGEQG 401 Lambda K H 0.324 0.139 0.421 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: 735 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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