Align tryptophan permease (characterized)
to candidate PP_3727 PP_3727 Amino-acid permease RocE
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__Putida:PP_3727 Length = 468 Score = 240 bits (613), Expect = 8e-68 Identities = 130/406 (32%), Positives = 225/406 (55%), Gaps = 11/406 (2%) Query: 72 SFDTSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTI 131 S + L R LK RH+ M+++GG IGTGLF+GSG I +GGP+G ++ + +AG + + Sbjct: 4 SVEKIQLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGLLMYLVM 63 Query: 132 HGLGEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNS 191 LGE++V+ PV G+F + T+++ P+ F++ +Y + W + LE AA M + W Sbjct: 64 VCLGELSVQMPVSGSFQAHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRWFP 123 Query: 192 SIDPVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHE 251 + W A+F V+ +N R FGEAE+ FS IK T+ GFI++ +++I G P Sbjct: 124 EVPIWYWSALFVVVLFGLNALATRAFGEAEYWFSGIKVATILGFIVIGLLVIFGAIPLSS 183 Query: 252 FIGAKYWHD---PGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIKQ 306 A ++ +G V +V++ Y+ G E+ +A+GET+ K +P A++ Sbjct: 184 GAPAPMLNNLVGESLFPHGLSAVFAVMMTVVYAFQGCEIMGVAAGETEHPEKSIPRAVRN 243 Query: 307 VFWRILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILI 366 V +R+L F+++++ ++ +VP+ L+ SPFV + I ++N VIL Sbjct: 244 VVFRVLIFYVLAIAVLSAIVPHEQAGLM------ESPFVQVFDMVGIPYAADLMNFVILT 297 Query: 367 SVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGS 426 ++LSVGNS ++AS+R L +M+ G+ P + + G PL + F L++ + + Sbjct: 298 AILSVGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALISLMTSFVA 357 Query: 427 MSEVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEF 472 +F LMA++G++ + W+ I L+ RFR A G L +L++ Sbjct: 358 ADTLFMVLMAVSGMSGTVTWIVIALAQYRFRKAWLRDGGQLQDLKY 403 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: 740 Number of extensions: 44 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: 468 Length adjustment: 35 Effective length of query: 557 Effective length of database: 433 Effective search space: 241181 Effective search space used: 241181 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