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 351943 BT2415 aspartate aminotransferase (NCBI ptt file)
Query= BRENDA::Q71RI9 (455 letters) >FitnessBrowser__Btheta:351943 Length = 397 Score = 157 bits (397), Expect = 6e-43 Identities = 115/360 (31%), Positives = 187/360 (51%), Gaps = 39/360 (10%) Query: 24 SSKVLGLCTSAKMALKFK-NAKRIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYV 82 S ++ L SA +A+ K N + +G+D V+NL G PD + P ++ Sbjct: 5 SDRLNSLSPSATLAMSQKSNELKAQGID---------------VINLSVGEPDFNTPDHI 49 Query: 83 KEELSKAAFIDNMNQYTRGFGHPALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNS 142 KE +K A DN ++Y+ G+PAL A+ K + +I A GA S+ N+ Sbjct: 50 KEA-AKKAIDDNFSRYSPVPGYPALRNAIVEKLKKENGLEYTA-AQISCANGAKQSVCNA 107 Query: 143 IQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELE 202 I LV+PGDEVI+ P++ Y MV+MA PV + + G++ D+ P++LE Sbjct: 108 ILVLVNPGDEVIVPAPYWVSYPEMVKMAEGTPVIV------SAGIE---QDFKITPKQLE 158 Query: 203 SKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKH-DTLCISDEVYEWLVYTGHTHV 261 + + KTKA+IL +P NP G VY+++EL +A + K+ + I+DE+YE + Y G H Sbjct: 159 AAITPKTKALILCSPSNPTGSVYSKEELAGLAAVLAKYPQVVVIADEIYEHINYIG-AHQ 217 Query: 262 KIATLPGMWERTITIGSAGKTFSVTGWKLGWSIGPAHLIKHLQTVQ-QNSFYTCATPLQA 320 IA P M ERT+ + K +++TGW++G+ GP ++K +Q Q + C+ +A Sbjct: 218 SIAQFPEMKERTVIVNGVSKAYAMTGWRIGFIAGPEWIVKACNKLQGQYTSGPCSVSQKA 277 Query: 321 ALAEAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLNSV-GLKPIVPDGGYFIIADVS 379 AEA ++ + + K E +RD +V+L V G + VP G +++ S Sbjct: 278 --AEAAYVGTQEP------VKEMQKAFERRRDLIVKLAKEVPGFEVNVPQGAFYLFPKCS 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: 405 Number of extensions: 26 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: 455 Length of database: 397 Length adjustment: 32 Effective length of query: 423 Effective length of database: 365 Effective search space: 154395 Effective search space used: 154395 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 Apr 09 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