Align Putative aspartate aminotransferase YhdR; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_072905149.1 BUB13_RS02385 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O07587 (393 letters) >NCBI__GCF_900142125.1:WP_072905149.1 Length = 393 Score = 353 bits (906), Expect = e-102 Identities = 171/389 (43%), Positives = 254/389 (65%), Gaps = 4/389 (1%) Query: 6 LSREVEENLNKGSWIRKLFDEGARLKKEFGEDQVFDFSLGNPIVEPPE---AFKRALIEE 62 ++ +V E + + SWIRK+F+EGA L++++G DQVFDF+LGNP +EPP+ A + + E Sbjct: 3 IAAKVNECIERASWIRKMFEEGAALREQYGADQVFDFTLGNPTIEPPKELHAELKRIAEN 62 Query: 63 AEKGSHGYIQNQGLLAAREKVAQFLGSRFEADFSAERIVMTVGAGGALNVALKSIVNPGE 122 E G H Y+ N G R VA+ + + + AE IVMT GAG A+NV LK+++NPG+ Sbjct: 63 PEPGMHRYMNNAGYDDTRAAVAEVIAEQCDQPVGAEHIVMTCGAGAAMNVVLKTLLNPGD 122 Query: 123 EVIILAPYFAEYKLYIENYGGKAVSCPLTSRFEIDIEAVRQSITPQTKGLILNTPHNPTG 182 EVIIL P+F EYK YI+N+ G V+ F+ DIEA+ +IT +TK +I+N+P+NPTG Sbjct: 123 EVIILTPFFVEYKFYIDNHQGIPVTVACKDDFQPDIEAIGAAITARTKAIIVNSPNNPTG 182 Query: 183 TVLSQKNIDDLGALLKEIEEKSGQTIYVLFDEPYSQLIYDEELANPFQSYHRVILASSFS 242 + + + +LG +LK+ E++ G I V+ DEPY+++ Y EE+ F ++ +S S Sbjct: 183 VIYPEATLKNLGEMLKQKEQEFGNAITVISDEPYAKISYGEEVPCIFNCIDNAVIVTSHS 242 Query: 243 KDLGIAGERLGYIGLDSRMPDADLLINAFVYCNRTLGFVNAPVMMQRAVARMDDLRVDAS 302 KDL + GER+GY+ M D +L + ++CNR LGFVNAP MMQR V + VD+ Sbjct: 243 KDLALPGERIGYLAASPAMDDINLFMQGAIFCNRVLGFVNAPAMMQRLVTNLQRSSVDSE 302 Query: 303 AYKERRDLMVDILKEAGFEFEMPKGGFFVFPKSPIEDEVAFCVHAAQKYKLLIVPSSGFG 362 Y+ +RD++ D L E GFE P GGF++FPKSP+ DE+ F + AQKY++L+VP SGFG Sbjct: 303 IYRRKRDMLYDKLTELGFEMIKPGGGFYLFPKSPMSDEMEF-IRLAQKYRILLVPGSGFG 361 Query: 363 MSGHFRLSFSVPIEQIKNSRDIFISLYKD 391 G FR+++ V + I+ S ++ L K+ Sbjct: 362 APGFFRIAYCVDDDMIERSLPLWEQLAKE 390 Lambda K H 0.320 0.139 0.396 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: 409 Number of extensions: 14 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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