Align valine/tyrosine/tryptophan amino-acid permease (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)
Query= CharProtDB::CH_091631 (619 letters) >FitnessBrowser__Keio:14712 Length = 458 Score = 214 bits (545), Expect = 6e-60 Identities = 140/436 (32%), Positives = 230/436 (52%), Gaps = 17/436 (3%) Query: 79 NSELESQEKNNLTKSIKSRHLVMISLGTGIGTGLLVGNGQVLGTAGPAGLVLGYGIASIM 138 + + S ++ L + + +RH+ +I+LG IGTGL +G G + AGPA ++LGYG+A I+ Sbjct: 8 SEDTASNQEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPA-VLLGYGVAGII 66 Query: 139 LYCIIQAAGELGLCYAGLTGNYTRYPSILVDPSLGFAVSVVYTIQWLTVLPLQLVTAAMT 198 + I++ GE+ + ++G++ + P GF Y + ++ V +L A + Sbjct: 67 AFLIMRQLGEM-VVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIY 125 Query: 199 VKYW-TSVNADIFVAVVFVFVIIINLFGSRGYAEAEFIFNSCKILMVIGFVILAIIINCG 257 ++YW V I+ A F+ + +NL R Y E EF F K+L +IG + + + Sbjct: 126 MQYWFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFS 185 Query: 258 GAGDRRYIGAEYWHNPGPFAHGFKGVCTVFCYAAFSYGGIEVLLLSAAEQENPTKSIPNA 317 G G + W G FA G+ G+ FS+GG+E++ ++AAE +P KSIP A Sbjct: 186 GHGGEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKA 245 Query: 318 CKKVVYRILLIYMLTTILVCFLVPYNSDELLGSSDSSGSHASPFVIAVASHGVKVVPHFI 377 +VVYRILL Y+ + +++ L P+ + S++SPFV+ + VV + Sbjct: 246 VNQVVYRILLFYIGSLVVLLALYPWVEVK---------SNSSPFVMIFHNLDSNVVASAL 296 Query: 378 NAVILISVISVANSSLYSGPRLLLSLAEQGVLPKCLAYVDRNGRPLLCFFVSLVFGCIGF 437 N VIL++ +SV NS +YS R+L L+ QG PK L V R G P+ +S + Sbjct: 297 NFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVV 356 Query: 438 VATSDAEEQVFTWLLAISSLSQLFIWMSMSLSHIRFRDAMAKQGRSMNEVGYKAQTGYWG 497 + ++ F L+A+ + L W+ + L+H+RFR AM +QGR E +KA +G Sbjct: 357 LINYLLPQKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQGR---ETQFKALLYPFG 413 Query: 498 SWL--AVLIAIFFLVC 511 ++L A L I L+C Sbjct: 414 NYLCIAFLGMILLLMC 429 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: 680 Number of extensions: 30 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: 619 Length of database: 458 Length adjustment: 35 Effective length of query: 584 Effective length of database: 423 Effective search space: 247032 Effective search space used: 247032 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