Align glutamine-pyruvate transaminase (EC 2.6.1.15); kynurenine-oxoglutarate transaminase (EC 2.6.1.7); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_011612267.1 TERY_RS13015 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_000014265.1:WP_011612267.1 Length = 387 Score = 143 bits (360), Expect = 1e-38 Identities = 110/347 (31%), Positives = 170/347 (48%), Gaps = 29/347 (8%) Query: 43 AKRIEGLDSNVWVE-FTKL----AADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQ 97 A R+ L + +E FTK + ++++L G PD P ++E +A D Sbjct: 4 ATRMNSLGGDAAIEVFTKAKQLESQGRNIIHLEIGQPDFKTPKNIREAAFQA-MNDGYTT 62 Query: 98 YTRGFGHPALVKALSCLYGKIYQ-RQIDPN-EEILVAVGAYGSLFNSIQGLVDPGDEVII 155 YT G L+K + I Q R I N +E++V GA +F ++ L++ GDEVI Sbjct: 63 YTPAAG---LLKLREVIAEHISQTRNISVNSDEVVVMPGAKPVIFFTLLALINSGDEVIY 119 Query: 156 MVPFYDCYEPMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILN 215 P + YE ++ + G P+ +PL + D+ F L + S KTK +I+N Sbjct: 120 PNPGFPVYESVINLVGGKPIPLPLLEE---------LDFQFSIDNLVNSISEKTKLLIIN 170 Query: 216 TPHNPLGKVYTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTIT 275 +PHNP G V T + L+ IA L VKH+ +SDE+Y L Y I + P M ERTI Sbjct: 171 SPHNPTGSVLTPEYLEAIAKLAVKHNFYVLSDEIYSHLNYDS-KFTSIISFPSMKERTIL 229 Query: 276 IGSAGKTFSVTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDD 335 + KT+++TGW+LG+SI P + + L + NS + Q A EA IK + Sbjct: 230 LDGHSKTYAMTGWRLGYSISPKAIAEKLDKLMLNSNSCACSFTQIAGIEA----IKNSQE 285 Query: 336 PECYFNSLPKELEVKRDRMVRLLNSV-GLKPIVPDGGYFIIADVSSL 381 + + E + +RD +V LNS+ G+ P G ++ +V L Sbjct: 286 ---FVKKIFAEFKQRRDVIVDGLNSISGINCRKPAGAFYAFPNVKQL 329 Lambda K H 0.320 0.136 0.419 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: 423 Number of extensions: 32 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: 455 Length of database: 387 Length adjustment: 32 Effective length of query: 423 Effective length of database: 355 Effective search space: 150165 Effective search space used: 150165 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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