Align tryptophan permease (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 209 bits (531), Expect = 3e-58 Identities = 133/395 (33%), Positives = 209/395 (52%), Gaps = 6/395 (1%) Query: 75 TSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGL 134 T +L+R LK RH+ +IA+GG+IGTGLF+GS + GP +++G+AI G + L Sbjct: 8 TGSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGP-SMILGYAIGGFIAFLIMRQL 66 Query: 135 GEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSID 194 GE+ V PV G+F+++ ++ F+ Y + + V E+ A VQ+W + Sbjct: 67 GEMIVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVP 126 Query: 195 PVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHEFIG 254 A F+ +I INL V+ FGE EF F+ +K + G I+L + L+ G + Sbjct: 127 TWATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKGGEQASI 186 Query: 255 AKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGE-TDPKG-LPSAIKQVFWRIL 312 + W G NGF G+L L + +S GG+E+ + + E +PK +P AI QV +RIL Sbjct: 187 SNLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRIL 246 Query: 313 FFFLISLTLVGFLVPYTNQNLLGGSSVD---NSPFVIAIKLHHIKALPSIVNAVILISVL 369 F++ +LT++ L P+ L G++ D SPFV L ++N V+L + L Sbjct: 247 IFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAAL 306 Query: 370 SVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSE 429 SV NS ++ +SR L +A QG P I+ G P++ + ++L LL V Sbjct: 307 SVYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQG 366 Query: 430 VFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQG 464 LM++A A I W I+L+H++FR AM+ QG Sbjct: 367 ALELLMSLAVAALVINWAMISLAHLKFRRAMQQQG 401 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: 739 Number of extensions: 53 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: 464 Length adjustment: 35 Effective length of query: 557 Effective length of database: 429 Effective search space: 238953 Effective search space used: 238953 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