Align Valine amino-acid permease; Branched-chain amino-acid permease 3 (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= SwissProt::P41815 (604 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 184 bits (468), Expect = 5e-51 Identities = 125/398 (31%), Positives = 203/398 (51%), Gaps = 17/398 (4%) Query: 86 LKKSMKSRHVVMMSLGTGIGTGLLVANAKGLSLAGPGSLVIGYVMVSFVTYFMVQAAGEM 145 L++ +K+RH+ +++LG IGTGL + A+ + LAGP S+++GY + + + +++ GEM Sbjct: 10 LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGP-SVLLGYAIAGLMAFLIMRQLGEM 68 Query: 146 GVTYPTLPGNFNAYNSIFISKSFGFATTWLFCIQWLTVLPLELITSSMTVKYWNDTINAD 205 V P + G+F+ + + S+ GF + W + + ++ V EL + V+YW Sbjct: 69 VVEEP-VAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTW 127 Query: 206 VFIVIFYVFLLFIHFFGVKAYGETEFIFNSCKILMVAGFIILSV-VINCGGAGVDGYIGG 264 IF+V + I+ VK YGE EF F K++ + I ++ G G D + Sbjct: 128 ATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLLGSGHGGPDASVAN 187 Query: 265 KYWRDPGSFAEGSGATRFKGICYILVSAYFSFGGIELFVLSINEQSNPRKSTPVAAKRSV 324 W+ G F G G+ L FSFGG+EL ++ E NPR+S P A + V Sbjct: 188 -LWQYGGFFPNG-----VTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVV 241 Query: 325 YRILIIYLLTMILIGFNVPHNNDQLMGSGGSATHASPYVLAASIHKVRVIPHIINAVILI 384 YRILI Y+ + ++ P Q + GGS P+V+ ++ I+N V+L Sbjct: 242 YRILIFYIGALAVLLSLYPW---QKVVQGGS-----PFVMIFHELDSDLVATILNIVVLT 293 Query: 385 SVISVANSALYAAPRLMCSLAQQGYAPKFLNYIDREGRPLRALVVCSLVGVVGFVACSPQ 444 + +SV NS +YA R++ LA QG AP+ L + R G PL AL V + + + Sbjct: 294 AALSVYNSCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLM 353 Query: 445 EEQAFTWLAAIAGLSELFTWSGIMLSHIRFRKAMKVQG 482 AF L A+A + + W+ I ++H++FRKA G Sbjct: 354 PGGAFGLLMALAVSALVINWASISITHLKFRKAKLAAG 391 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: 593 Number of extensions: 25 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: 453 Length adjustment: 35 Effective length of query: 569 Effective length of database: 418 Effective search space: 237842 Effective search space used: 237842 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