Align valine/tyrosine/tryptophan amino-acid permease (characterized)
to candidate BWI76_RS07360 BWI76_RS07360 phenylalanine transporter
Query= CharProtDB::CH_091631 (619 letters) >FitnessBrowser__Koxy:BWI76_RS07360 Length = 458 Score = 208 bits (529), Expect = 5e-58 Identities = 138/436 (31%), Positives = 230/436 (52%), Gaps = 17/436 (3%) Query: 79 NSELESQEKNNLTKSIKSRHLVMISLGTGIGTGLLVGNGQVLGTAGPAGLVLGYGIASIM 138 +SE + L + +++RH+ +I+LG IGTGL +G G + AGPA ++LGY +A I+ Sbjct: 7 SSETIEESGPTLHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPA-VLLGYAVAGIV 65 Query: 139 LYCIIQAAGELGLCYAGLTGNYTRYPSILVDPSLGFAVSVVYTIQWLTVLPLQLVTAAMT 198 + I++ GE+ + ++G++ + P GF Y + ++ V +L A + Sbjct: 66 AFLIMRQLGEM-VVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIY 124 Query: 199 VKYWT-SVNADIFVAVVFVFVIIINLFGSRGYAEAEFIFNSCKILMVIGFVILAIIINCG 257 ++YW V I+ A F+ + +NL R Y EAEF F K+L +IG + + + G Sbjct: 125 MQYWLPDVPTWIWAAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMIGFGLWMLFG 184 Query: 258 GAGDRRYIGAEYWHNPGPFAHGFKGVCTVFCYAAFSYGGIEVLLLSAAEQENPTKSIPNA 317 G G + W + G FA G+ G+ FS+GG+E++ ++AAE +NP KSIP A Sbjct: 185 GHGGSKAGIDNLWKHGGFFATGWHGLIMSLAVIMFSFGGLELIGITAAEAQNPEKSIPKA 244 Query: 318 CKKVVYRILLIYMLTTILVCFLVPYNSDELLGSSDSSGSHASPFVIAVASHGVKVVPHFI 377 +VVYRILL Y+ + +++ L P+ + S +SPFV+ + VV + Sbjct: 245 VNQVVYRILLFYIGSLVVLLALYPWVEIQ---------SDSSPFVMIFHNLDSNVVASAL 295 Query: 378 NAVILISVISVANSSLYSGPRLLLSLAEQGVLPKCLAYVDRNGRPLLCFFVSLVFGCIGF 437 N VIL++ +SV NS +YS R+L L+ QG PK LA V + G P+ +S + + Sbjct: 296 NFVILVASLSVYNSGVYSNSRMLFGLSVQGNAPKFLARVSKRGVPVNSLLLSGIITSLVV 355 Query: 438 VATSDAEEQVFTWLLAISSLSQLFIWMSMSLSHIRFRDAMAKQGRSMNEVGYKAQTGYWG 497 V ++ L+A+ + L W+ + L+H++FR A ++GR E +KA Sbjct: 356 VLNYLLPQKALGLLMALVVATLLLNWIMICLAHLKFRAAQRRKGR---EPKFKALLSPAS 412 Query: 498 SW--LAVLIAIFFLVC 511 ++ +A L I L+C Sbjct: 413 NYICIAFLALILVLMC 428 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: 707 Number of extensions: 29 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: 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