Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_043743690.1 AMB_RS07030 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::Q9HUI9 (393 letters) >NCBI__GCF_000009985.1:WP_043743690.1 Length = 384 Score = 166 bits (419), Expect = 1e-45 Identities = 116/366 (31%), Positives = 173/366 (47%), Gaps = 6/366 (1%) Query: 19 DIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRI 78 D+ A AR G +++ L VG P P ++ AA ++ Y G+ +LR+RI Sbjct: 18 DVMRDAAARQAAGADVIHLEVGQPSGQAPPKVLDAAARAVRTEPLGYTLALGRDSLRERI 77 Query: 79 AERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGA 138 A + + G +V E+V V G+ A PGD V VA P Y Y + + G Sbjct: 78 ARHYHQAYGVSVVPERVCVTTGSSAAFLLAFLAAFEPGDRVAVAAPGYPAYRNILESLGV 137 Query: 139 RVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHD 198 V VPV + +++ A EV A + R + + SP NP+G+ L LA C H Sbjct: 138 ECVLVPVGPSSRWQITA-EVLAGVEGRLDGVVVASPSNPTGSMLSAHEVAELAGWCELHG 196 Query: 199 LWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAH 258 + +ISDE+Y + + G + A+ A +NS SK +AMTGWR+GW+V P L Sbjct: 197 IRLISDEIYHGITY-GRAAATAAGMAAAPHAVVINSFSKYYAMTGWRLGWMVLPEDLARS 255 Query: 259 LENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRP 318 +E L LY SP + A ++ + ELEA AYR RD+++ L + R Sbjct: 256 VECLTQ-NLYISPPTLSQVAAESVFDCIDELEARVAAYRANRDILVAELPKAGFDRLAPS 314 Query: 319 DGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGH--IRLGLVLGAEPLR 376 DG ++ D+ ++ F R+L GV+ G F P GH +R AE + Sbjct: 315 DGAFYLYADVSEMTNDSREFCARMLAETGVACTPGVDFDP-IEGHRTLRFSYAGSAEHMA 373 Query: 377 EACRRI 382 EA RR+ Sbjct: 374 EAARRL 379 Lambda K H 0.322 0.136 0.411 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: 402 Number of extensions: 18 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: 393 Length of database: 384 Length adjustment: 30 Effective length of query: 363 Effective length of database: 354 Effective search space: 128502 Effective search space used: 128502 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 (21.9 bits) S2: 50 (23.9 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