Align valine/tyrosine/tryptophan amino-acid permease (characterized)
to candidate PP_3727 PP_3727 Amino-acid permease RocE
Query= CharProtDB::CH_091631 (619 letters) >FitnessBrowser__Putida:PP_3727 Length = 468 Score = 231 bits (590), Expect = 4e-65 Identities = 125/413 (30%), Positives = 225/413 (54%), Gaps = 14/413 (3%) Query: 83 ESQEKNNLTKSIKSRHLVMISLGTGIGTGLLVGNGQVLGTAGPAGLVLGYGIASIMLYCI 142 +S EK LT+++KSRH+ M+SLG IGTGL +G+G + GP G +L Y +A +++Y + Sbjct: 3 DSVEKIQLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGLLMYLV 62 Query: 143 IQAAGELGLCYAGLTGNYTRYPSILVDPSLGFAVSVVYTIQWLTVLPLQLVTAAMTVKYW 202 + GEL + ++G++ + + + P+ GF + VY + W T + L+ A M + W Sbjct: 63 MVCLGELSV-QMPVSGSFQAHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRW 121 Query: 203 TSVNADIFVAVVFVFVII-INLFGSRGYAEAEFIFNSCKILMVIGFVILAIIINCGGAGD 261 + + +FV V+ +N +R + EAE+ F+ K+ ++GF+++ +++ G Sbjct: 122 FPEVPIWYWSALFVVVLFGLNALATRAFGEAEYWFSGIKVATILGFIVIGLLVIFGAIPL 181 Query: 262 RRYIGAEYWHN---PGPFAHGFKGVCTVFCYAAFSYGGIEVLLLSAAEQENPTKSIPNAC 318 A +N F HG V V +++ G E++ ++A E E+P KSIP A Sbjct: 182 SSGAPAPMLNNLVGESLFPHGLSAVFAVMMTVVYAFQGCEIMGVAAGETEHPEKSIPRAV 241 Query: 319 KKVVYRILLIYMLTTILVCFLVPYNSDELLGSSDSSGSHASPFVIAVASHGVKVVPHFIN 378 + VV+R+L+ Y+L ++ +VP+ + +G SPFV G+ +N Sbjct: 242 RNVVFRVLIFYVLAIAVLSAIVPH---------EQAGLMESPFVQVFDMVGIPYAADLMN 292 Query: 379 AVILISVISVANSSLYSGPRLLLSLAEQGVLPKCLAYVDRNGRPLLCFFVSLVFGCIGFV 438 VIL +++SV NS LY+ R+L ++++ G+ PK L+ + + G PL ++L F I + Sbjct: 293 FVILTAILSVGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALISLM 352 Query: 439 ATSDAEEQVFTWLLAISSLSQLFIWMSMSLSHIRFRDAMAKQGRSMNEVGYKA 491 + A + +F L+A+S +S W+ ++L+ RFR A + G + ++ YKA Sbjct: 353 TSFVAADTLFMVLMAVSGMSGTVTWIVIALAQYRFRKAWLRDGGQLQDLKYKA 405 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: 662 Number of extensions: 31 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: 619 Length of database: 468 Length adjustment: 35 Effective length of query: 584 Effective length of database: 433 Effective search space: 252872 Effective search space used: 252872 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 (21.5 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