Align tryptophan permease (characterized)
to candidate RR42_RS05070 RR42_RS05070 amino acid permease
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__Cup4G11:RR42_RS05070 Length = 466 Score = 202 bits (515), Expect = 2e-56 Identities = 129/394 (32%), Positives = 202/394 (51%), Gaps = 14/394 (3%) Query: 78 LKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGEI 137 L R+LKP L MIAIGG+IGTGLF+GSG AI GP GV++ +AI + + L E+ Sbjct: 8 LHRSLKPAQLAMIAIGGAIGTGLFMGSGFAIGFAGP-GVLLSYAIGALVTLLLMGCLAEM 66 Query: 138 TVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPVI 197 TV P G+F Y ++ P F+V Y + E+ A A+ + YW + Sbjct: 67 TVAHPTSGSFGAYAEHYVSPLAGFLVRYAYWASIVLAVGTEVTAVALYMGYWFPQVPAWF 126 Query: 198 WVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICG--GGPDHEFIGA 255 W+ F A ++ INL GV FG E+ FS +K + + FI++ ++ G G GA Sbjct: 127 WIVSFSAALILINLVGVGIFGAVEYLFSMVKIVAIVAFILVAAYIVFGAPGSTGSGAAGA 186 Query: 256 KYWH---DPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET-DP-KGLPSAIKQVFWR 310 + H G L NG G+ ++V+ +S IEM +A+GE DP + + A + R Sbjct: 187 GFHHYTAHGGFLPNGLWGMWVAVIVSIFSYLSIEMIAVAAGEAQDPERAVLQAFRSTMIR 246 Query: 311 ILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISVLS 370 + F+L++L L+ +VP+ + SPFV ++ H+ +I+N V+LI+ LS Sbjct: 247 LGLFYLLTLALMLAIVPWNQ------AGAQKSPFVQVMEAIHVPGAAAIINFVVLIAALS 300 Query: 371 VGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMSEV 430 NS ++ ++RT+ S+A G P FG + + G P+ ++ +S+ LA + Sbjct: 301 AMNSQLYITTRTMFSLARAGQAPRSFGEVSKRGIPVRALLLSSIGIALATGLNVFYPGNA 360 Query: 431 FNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQG 464 F +MAI+ W I ++H RFR A G Sbjct: 361 FLLMMAISMFGALFTWFMIFVTHYRFRRQWAAAG 394 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: 679 Number of extensions: 40 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: 592 Length of database: 466 Length adjustment: 35 Effective length of query: 557 Effective length of database: 431 Effective search space: 240067 Effective search space used: 240067 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