Align tryptophan permease (characterized)
to candidate PP_0660 PP_0660 S-methyl-L-methionine transporter
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__Putida:PP_0660 Length = 479 Score = 215 bits (548), Expect = 3e-60 Identities = 127/398 (31%), Positives = 212/398 (53%), Gaps = 10/398 (2%) Query: 79 KRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGEIT 138 K+ ++ RH++M+A+GG IGTGLF+ SG + + GPLG VI + + + + LGE+ Sbjct: 17 KQDMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPLGAVIAYILGAIMVYLVMMCLGELA 76 Query: 139 VRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPVIW 198 V P VG+F++Y TR+L P ++V+ +Y L W + E AA + + W +W Sbjct: 77 VHMPEVGSFSSYATRYLGPGTGYMVAWMYWLTWTVAIGSEFTAAGILMVRWFPDTPVWMW 136 Query: 199 VAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHE--FIGAK 256 A+F A + N+ VR F E EF S +K + V F+++ I GG + G Sbjct: 137 SALFGAAVFISNIISVRSFAETEFWLSLVKVLAVIAFLVVGGGAILGGFEIQQAHSAGLG 196 Query: 257 YWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET-DP-KGLPSAIKQVFWRILFF 314 + G GF + L+ +++ G E+ +A+GET DP K +P AI+ R+ F Sbjct: 197 NFTREGLFPTGFWSIAMTLLAVAFAFSGTELIGIAAGETKDPEKNVPKAIRTTVLRLALF 256 Query: 315 FLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLSVGNS 374 F+ ++ ++ L+P + V SPFV+ + I I+N VI+ ++LS NS Sbjct: 257 FIGTIFVLATLLPREQ------AGVIESPFVMVFAMIGIPYAADIMNFVIITALLSAANS 310 Query: 375 CIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEVFNWL 434 ++A+SR L +++ QG +P + + R G P I+ + G+ + L + ++ L Sbjct: 311 GLYAASRMLWTLSDQGNMPRRYATLSRRGTPFNAIVLSMAGGMASLLSSVFAPDTIYLAL 370 Query: 435 MAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEF 472 ++I+GLA +VW+SI S I FR A G L++L+F Sbjct: 371 VSISGLAVVVVWISIAASQIAFRRHYIASGGKLEDLKF 408 Lambda K H 0.326 0.141 0.447 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: 749 Number of extensions: 39 Number of successful extensions: 4 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: 592 Length of database: 479 Length adjustment: 35 Effective length of query: 557 Effective length of database: 444 Effective search space: 247308 Effective search space used: 247308 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 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