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_073036174.1 BUB04_RS01205 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q71RI9 (455 letters) >NCBI__GCF_900129305.1:WP_073036174.1 Length = 389 Score = 210 bits (535), Expect = 6e-59 Identities = 121/377 (32%), Positives = 195/377 (51%), Gaps = 29/377 (7%) Query: 67 VNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGHPALVKALSCLYGKIYQRQIDPN 126 +NL QG D+ P V+ ++ A + N YTR G L +A++ + + ++DP Sbjct: 30 INLSQGVCDLEIPEPVRRG-AQQAIDEGYNVYTRYDGLQELREAIAHKHKQFNGLEVDPE 88 Query: 127 EEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLRSKPTDG 186 E++V+ G G+ + + L++PGDEVI+ P+Y + + A P ++ L Sbjct: 89 GEVIVSAGTTGAFYCACLALLEPGDEVIVFEPYYGYHISTLLATQARPAYVRLHPP---- 144 Query: 187 MKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKHDTLCIS 246 WTF +LE+ +S+T+ I++NTP NP GKV+TR+EL+ I +HD + Sbjct: 145 ------GWTFTEEDLEAAVTSRTRGILVNTPANPSGKVFTREELEAIGRFATRHDLFIFT 198 Query: 247 DEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFSVTGWKLGWSIGPAHLIKHLQTV 306 DE+YE+ VY G HV A + G+ ERTITI KTFS+TGW++G+ I + + Sbjct: 199 DEIYEYFVYDGRRHVPPAAIEGIGERTITISGLSKTFSITGWRIGYCICDRKWARPIGWF 258 Query: 307 QQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLNSVGLKPI 366 + PLQ +A + ++D Y+ + +E + KRDR+ L GL P+ Sbjct: 259 NDLVYVCAPAPLQIGVARG----LLQLD--AGYYQQIAREYQEKRDRICDALTRAGLDPV 312 Query: 367 VPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTKHKKLTAIPVSAFCDSKSKPHFE 426 VP G Y+++AD+S L D S + ++ + + A+P AF ++ Sbjct: 313 VPQGAYYVLADISRLPGDASKDKA---------MFLLQETGVAAVPGEAFYHDEAG---S 360 Query: 427 KLVRFCFIKKDSTLDAA 443 +L RFCF K+D LD A Sbjct: 361 QLARFCFAKRDQVLDEA 377 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: 436 Number of extensions: 19 Number of successful extensions: 4 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: 389 Length adjustment: 32 Effective length of query: 423 Effective length of database: 357 Effective search space: 151011 Effective search space used: 151011 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