Align tryptophanase (EC 4.1.99.1) (characterized)
to candidate 351020 BT1492 tyrosine phenol-lyase (NCBI ptt file)
Query= BRENDA::E9RK37 (458 letters) >FitnessBrowser__Btheta:351020 Length = 459 Score = 741 bits (1912), Expect = 0.0 Identities = 355/457 (77%), Positives = 406/457 (88%) Query: 1 MEIPFAESWKIKMIEPIKKSTREEREQWLKEAHYNVFQLKAEQVYIDLLTDSGTGSMSDR 60 ME+PFAESWKIKM+EPI+KSTREEREQW+KEAHYNVFQLK+EQVYIDL+TDSGTG+MSDR Sbjct: 1 MELPFAESWKIKMVEPIRKSTREEREQWIKEAHYNVFQLKSEQVYIDLITDSGTGAMSDR 60 Query: 61 QWAAMMLGDESYAGATSFYKFEETVQKILGMKYIIPTHQGRAAENVLFSYLVKEGNVIPG 120 QWA MMLGDESYAGATSF+K ++T+ +I G +YIIPTHQGRAAENVLFSYLV EGN++PG Sbjct: 61 QWAGMMLGDESYAGATSFFKLKDTITRITGFEYIIPTHQGRAAENVLFSYLVHEGNIVPG 120 Query: 121 NAHFDTTKGHIESRKAHAIDVTTDDAKDTQKEVPFKGNVCLKKLEKVLQENKGNVPFMVL 180 N+HFDTTKGHIE R A A+D T D+AK+TQ E+PFKGNV KLEK L E +PF+++ Sbjct: 121 NSHFDTTKGHIEGRHAIALDCTIDEAKNTQLEIPFKGNVDPAKLEKALSEYADRIPFIIV 180 Query: 181 TVTNNTVGGQPVSMKNIKETCALCHQYGIPVVMDSARFAENAYFIKVREEGYADKSIKEI 240 T+TNNT GGQPVSM+N++E A+ ++Y PV+ DSARFAENAYFIK+RE+GY DKSIKEI Sbjct: 181 TITNNTAGGQPVSMQNLREVRAIANKYNKPVLFDSARFAENAYFIKMREKGYQDKSIKEI 240 Query: 241 VREMYAEADAATMSAKKDGVVNMGGFIATNNKEWFEGAKMFCIPMEGYVTYGGMSGRDLN 300 REM+ AD TMSAKKDG+VNMGGFIAT KEW+EGAK FC+ EGY+TYGGM+GRD+N Sbjct: 241 TREMFDLADGMTMSAKKDGIVNMGGFIATRRKEWYEGAKGFCVQYEGYLTYGGMNGRDMN 300 Query: 301 ALAQGLDENTEFDMLQTRIHQVEYLAKKLDEYGIPYQRPAGGHAIFVDASKVLTHVPKEE 360 ALA GLDENTEFD L+TRI QVEYLA+KLDEY IPYQRPAGGHAIFVDASKVLTHVPKEE Sbjct: 301 ALAIGLDENTEFDNLETRIKQVEYLAQKLDEYEIPYQRPAGGHAIFVDASKVLTHVPKEE 360 Query: 361 FPAQTLTCELYLEAGIRGVEVGYMLADRDPETGENRFGGLDLLRLAIPRRVYTDNHMNVI 420 FPAQTLT ELYLEAGIRG E+GY+LADRDP T ENRF GLDLLRLAIPRRVYTDNHMNVI Sbjct: 361 FPAQTLTVELYLEAGIRGCEIGYILADRDPITHENRFNGLDLLRLAIPRRVYTDNHMNVI 420 Query: 421 AAAVKKVFDRRESVTRGVAIEWEAPLMRHFTVQLKRL 457 AAA++ VF+RRE++TRGV I WEAPLMRHFTVQL+RL Sbjct: 421 AAALRNVFERRETITRGVRIAWEAPLMRHFTVQLERL 457 Lambda K H 0.318 0.134 0.393 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: 781 Number of extensions: 16 Number of successful extensions: 1 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: 458 Length of database: 459 Length adjustment: 33 Effective length of query: 425 Effective length of database: 426 Effective search space: 181050 Effective search space used: 181050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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