Align Tryptophanase; EC 4.1.99.1; L-tryptophan indole-lyase; TNase (uncharacterized)
to candidate WP_004317762.1 C665_RS14635 tryptophanase/L-cysteine desulfhydrase PLP-dependent
Query= curated2:Q8R9K5 (462 letters) >NCBI__GCF_000310185.1:WP_004317762.1 Length = 482 Score = 343 bits (881), Expect = 5e-99 Identities = 185/452 (40%), Positives = 269/452 (59%), Gaps = 3/452 (0%) Query: 10 EPYKIKMVEPLKITTREERIRLIKEAGYNLFLLKSDDVYIDLLTDSGTAAMSDYQWAGMM 69 E +K+++V+ L + E R+ I EAG N FLL++ DV++D+LTDSG AMSD Q A MM Sbjct: 15 EMHKVRIVQKLNLPPVERRLEAITEAGNNTFLLRNADVFMDMLTDSGVNAMSDQQLAAMM 74 Query: 70 LGDESYAGSRNYQHLCEVVQDIFGYKYVVPTHQGRGAEKVLFPLLIKKGQYVLGNMHFDT 129 + D+SYAGS Y L + +IFG + +P HQGR E +L +L+ G V N HF T Sbjct: 75 IADDSYAGSATYTRLENKLHEIFGMPFFLPAHQGRACENILAQVLVSPGSVVPMNYHFTT 134 Query: 130 TKAHIELAGGIGIDMVIKEAEDTENYHPFKGNFDVEALENFIKEKGAENIAFILATVTCN 189 TKAHI L GG ++V + + HPFKGN DV L + I GA+ IAF+ N Sbjct: 135 TKAHITLNGGKVEELVADVGLEVVSVHPFKGNMDVAKLRDVIGLHGADKIAFVRMEAGTN 194 Query: 190 SAGGQPVSMENIKEVRRIADKYGIRLFFDAARFAENAYFIKQREKGYENKSIKEIVREMF 249 GGQP S++N+ ++RR+ D++G+ L DA+ A+N +FIK+RE+ + SI++I R M Sbjct: 195 LIGGQPFSVQNLADIRRVCDEFGLMLVMDASLLADNLHFIKEREEACKGLSIRDITRRMA 254 Query: 250 SYGDGFTMSAKKDALVNIGGLIAIKEDEELFTRVKTMLIPMEGFVTYGGLAGRDMEAMAR 309 D SA+K GG+ EEL+ R++ ++ EGF+TYGG++ R+MEA+ Sbjct: 255 DLCDVIYFSARKLGCARGGGMCI--RSEELYRRMRGLVPLYEGFLTYGGMSVREMEALTV 312 Query: 310 GLEEVLDENYLAWRINQVKYLGDKLREAGIPIQYPTGGHAVFIDGKKFLPHVPQEQFPSH 369 GLEE +DE + + ++ D+L + GIP+ P GG I+ +F+ HVPQ Q+P+ Sbjct: 313 GLEETMDEEVINQGPQFIGFMVDELVKRGIPVITPAGGLGCHINAMQFVDHVPQAQYPAG 372 Query: 370 AICVELYIEAGIRAVEVGALLAGRDPETGQNRLPKLDFVRLTIPRRVYTNSHMDVVAEAV 429 A+ LY+ GIR +E G L R+P+ G ++ VRL +PRRV+T S + + + Sbjct: 373 ALASALYLAGGIRGMERGTLSEQREPD-GTELFANMELVRLALPRRVFTLSQVKYAVDRL 431 Query: 430 KRVYARRDQIKGYRFVYEPPILRHFTARLEPV 461 + +YA R I G F EP ILR F RL PV Sbjct: 432 EWLYANRRLIGGLVFTEEPEILRFFYGRLAPV 463 Lambda K H 0.321 0.140 0.407 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: 570 Number of extensions: 22 Number of successful extensions: 3 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: 462 Length of database: 482 Length adjustment: 33 Effective length of query: 429 Effective length of database: 449 Effective search space: 192621 Effective search space used: 192621 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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