Align Valine amino-acid permease; Branched-chain amino-acid permease 3 (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)
Query= SwissProt::P41815 (604 letters) >FitnessBrowser__Keio:14258 Length = 457 Score = 196 bits (497), Expect = 2e-54 Identities = 120/405 (29%), Positives = 204/405 (50%), Gaps = 15/405 (3%) Query: 78 KSMKSNNHLKKSMKSRHVVMMSLGTGIGTGLLVANAKGLSLAGPGSLVIGYVMVSFVTYF 137 + + LK+ +K+RH+ +++LG IGTGL + +A + AGPG +++GY + F+ + Sbjct: 3 EGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPG-IILGYAIAGFIAFL 61 Query: 138 MVQAAGEMGVTYPTLPGNFNAYNSIFISKSFGFATTWLFCIQWLTVLPLELITSSMTVKY 197 +++ GEM V P + G+F+ + + GFA+ W + + ++ V EL +++ Sbjct: 62 IMRQLGEMVVEEP-VAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQF 120 Query: 198 WNDTINADVFIVIFYVFLLFIHFFGVKAYGETEFIFNSCKILMVAGFIILSVVINCGGAG 257 W I V +F+V + I+ VK +GE EF F K++ V II + G G Sbjct: 121 WYPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNG 180 Query: 258 VDGYIGGKYWRDPGSFAEGSGATRFKGICYILVSAYFSFGGIELFVLSINEQSNPRKSTP 317 W G G F G+ ++ FSFGG+EL ++ E NP +S P Sbjct: 181 GPQATVSNLWDQGGFLPHG-----FTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIP 235 Query: 318 VAAKRSVYRILIIYLLTMILIGFNVPHNNDQLMGSGGSATHASPYVLAASIHKVRVIPHI 377 A + +YRILI Y+ ++ ++ +P SP+VL + + Sbjct: 236 KATNQVIYRILIFYIGSLAVLLSLMPWTR--------VTADTSPFVLIFHELGDTFVANA 287 Query: 378 INAVILISVISVANSALYAAPRLMCSLAQQGYAPKFLNYIDREGRPLRALVVCSLVGVVG 437 +N V+L + +SV NS +Y R++ LAQQG APK L +D+ G P+ ++V +LV + Sbjct: 288 LNIVVLTAALSVYNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALC 347 Query: 438 FVACSPQEEQAFTWLAAIAGLSELFTWSGIMLSHIRFRKAMKVQG 482 + E AF L A+ + + W+ I L+H++FR+A + QG Sbjct: 348 VLINYLAPESAFGLLMALVVSALVINWAMISLAHMKFRRAKQEQG 392 Lambda K H 0.324 0.138 0.420 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: 608 Number of extensions: 23 Number of successful extensions: 6 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: 604 Length of database: 457 Length adjustment: 35 Effective length of query: 569 Effective length of database: 422 Effective search space: 240118 Effective search space used: 240118 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