Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_043743690.1 AMB_RS07030 1-aminocyclopropane-1-carboxylate deaminase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000009985.1:WP_043743690.1 Length = 384 Score = 171 bits (432), Expect = 4e-47 Identities = 121/374 (32%), Positives = 176/374 (47%), Gaps = 11/374 (2%) Query: 10 AMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAG 69 A+ P + V A + G D++ L G+P P V +AA RA+ Y G Sbjct: 10 AIAPFIVMDVMRDAAARQAAGADVIHLEVGQPSGQAPPKVLDAAARAVRTEPLGYTLALG 69 Query: 70 IPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYP 129 LRE +A + + G+SV PE VT G A F A +PGD V V +P + +Y Sbjct: 70 RDSLRERIARHYHQAYGVSVVPERVCVTTGSSAAFLLAFLAAFEPGDRVAVAAPGYPAYR 129 Query: 130 EMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEAL 189 ++ G V V P + E V + R +VV SP+NPTG++ + L Sbjct: 130 NILESLGVECVLVPVGPSSRWQITAE-VLAGVEGRLDGVVVASPSNPTGSMLSAHEVAEL 188 Query: 190 ARLAVEHDFYLVSDEIYEHLLY-EGEHFSPGRVAPEHTLTVNGAAKAFAMTGWRIGYACG 248 A H L+SDEIY + Y + G A H + +N +K +AMTGWR+G+ Sbjct: 189 AGWCELHGIRLISDEIYHGITYGRAAATAAGMAAAPHAVVINSFSKYYAMTGWRLGWMVL 248 Query: 249 PKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLT 308 P+++ +++ ++ SP T++Q A + A V AYR RD+L+ L Sbjct: 249 PEDLARSVECLTQNLYISPPTLSQVAAESVFDCIDELEARV----AAYRANRDILVAELP 304 Query: 309 ALGLKAVRPS-GAFYVLMDTSPIAPDEVRAAERLL-EAGVAVVPGTDFAAF-GH--VRLS 363 G + PS GAFY+ D S + D R+L E GVA PG DF GH +R S Sbjct: 305 KAGFDRLAPSDGAFYLYADVSEMTNDSREFCARMLAETGVACTPGVDFDPIEGHRTLRFS 364 Query: 364 YATSEENLRKALER 377 YA S E++ +A R Sbjct: 365 YAGSAEHMAEAARR 378 Lambda K H 0.317 0.133 0.379 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: 334 Number of extensions: 20 Number of successful extensions: 6 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: 385 Length of database: 384 Length adjustment: 30 Effective length of query: 355 Effective length of database: 354 Effective search space: 125670 Effective search space used: 125670 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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