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_005452968.1 SACCYDRAFT_RS01550 putative succinyldiaminopimelate transaminase DapC
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_000244975.1:WP_005452968.1 Length = 386 Score = 236 bits (603), Expect = 7e-67 Identities = 152/406 (37%), Positives = 215/406 (52%), Gaps = 30/406 (7%) Query: 44 KRIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFG 103 +R+ S ++ E T LA S VNLGQGFPD P + E A F NQY G G Sbjct: 8 ERLRPFTSTIFAEMTALATRTSAVNLGQGFPDTDGPEGMLEAARNALF-GGANQYPPGPG 66 Query: 104 HPALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCY 163 P L +A++ + Y + DP+ EILV GA ++ S+ L PGDEVI++ P+YD Y Sbjct: 67 RPELREAIAAHRAR-YGTEYDPDGEILVTAGATEAIAASLLALTGPGDEVIVIEPYYDSY 125 Query: 164 EPMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGK 223 V MAGA + L DG ++ D + + + T+AI++N+PHNP G Sbjct: 126 AAAVAMAGATRRVVSL---VPDGDRFA-----LDLDAVRAAVNPNTRAILVNSPHNPTGT 177 Query: 224 VYTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTF 283 V TR EL +A+LCV+ D L I+DEVYE LV+ H+ +AT PGM RT++I SAGKTF Sbjct: 178 VLTRTELAGLAELCVERDLLAITDEVYEHLVFDDAEHLPLATFPGMSSRTVSISSAGKTF 237 Query: 284 SVTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSL 343 + TGWK+GW P L ++ +Q + PLQ A+A A ++ + SL Sbjct: 238 NCTGWKIGWVCAPRELTAAVRAAKQFLTFVSGGPLQPAVAHALRHELP-------WVESL 290 Query: 344 PKELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKW-M 402 + L+ KRDR+ L G G YF+ ADV LG N++E + W + Sbjct: 291 RESLQAKRDRLCAGLADAGFAVRPGAGTYFVCADVRPLGF----TNAEE------LAWRL 340 Query: 403 TKHKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFR 448 + + A+PVS F D + ++ L+RF F K++ LD A E R Sbjct: 341 PESIGVAAVPVSVFTDHPEE--WQHLLRFAFCKREEVLDEAIERLR 384 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: 417 Number of extensions: 22 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: 386 Length adjustment: 32 Effective length of query: 423 Effective length of database: 354 Effective search space: 149742 Effective search space used: 149742 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