Align tryptophan permease (characterized)
to candidate WP_003943879.1 C1M55_RS01060 amino acid permease
Query= CharProtDB::CH_091156 (592 letters) >NCBI__GCF_002893965.1:WP_003943879.1 Length = 469 Score = 226 bits (575), Expect = 2e-63 Identities = 139/400 (34%), Positives = 223/400 (55%), Gaps = 10/400 (2%) Query: 72 SFDTSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTI 131 S D L+ TLK RHL MIAI G IG GLFVGSG AI E GP GV+I +A+AG +I + Sbjct: 3 STDQPALQHTLKKRHLSMIAIAGVIGAGLFVGSGVAIQETGP-GVLISYALAGVVVILVM 61 Query: 132 HGLGEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNS 191 LGE++ P G+F++Y + + F + +Y W VL +E A A+ + W Sbjct: 62 RMLGEMSAASPETGSFSSYADKAIGRWAGFSIGWLYAWFWIIVLGIEATAGALIMNRWVP 121 Query: 192 SIDPVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHE 251 + W I V+ N+ V+ FGE EF F++IK + + F+ + +V ICG P E Sbjct: 122 GVPQWTWALILMIVLTLTNIISVKSFGEFEFWFASIKVVAIIAFLGMGIVAICGWMPGVE 181 Query: 252 FIG-AKYWHDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGET-DP-KGLPSAIKQVF 308 G G L NG +L+ ++V +S G E+ +A+GE+ +P + + +A+K V Sbjct: 182 APGMTNLTGHGGFLPNGTGAMLAAVLVVVFSFFGAEIATIAAGESANPLEAVRAAVKSVV 241 Query: 309 WRILFFFLISLTLVGFLVPYTNQNLLGGSSVDNSPFVIAIKLHHIKALPSIVNAVILISV 368 WRIL F++ S+ +V L+P+ + +SV SP+V + + I A +I++ V+L SV Sbjct: 242 WRILIFYIGSIAVVVTLLPWDS------ASVALSPYVAVMDSYGIPAAGNIMDVVVLTSV 295 Query: 369 LSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMS 428 LS NS ++ +SR + S+A +G P I++ G P+ ++ +++ G L + S Sbjct: 296 LSCLNSGLYTASRMIFSLAGRGDAPKSLSRIEKTGVPMRAVLVSTIVGFLTVGMNYLSPD 355 Query: 429 EVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLD 468 +VF +L+ +G VWL I++S +R R ++A G+ L+ Sbjct: 356 KVFLFLVNSSGAIALFVWLVISVSQLRTRRKLEASGQELE 395 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: 681 Number of extensions: 43 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: 592 Length of database: 469 Length adjustment: 35 Effective length of query: 557 Effective length of database: 434 Effective search space: 241738 Effective search space used: 241738 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 24 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