Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_037580662.1 BS73_RS22465 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= CharProtDB::CH_004890 (393 letters) >NCBI__GCF_000744815.1:WP_037580662.1 Length = 419 Score = 149 bits (375), Expect = 2e-40 Identities = 121/392 (30%), Positives = 186/392 (47%), Gaps = 29/392 (7%) Query: 13 STTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGHTKYTPSGGLAEL 72 S TLAI + +AAG V+ LG GE P + AAV + Y P G AE Sbjct: 5 SATLAIDETLRARRAAGEKVLHLGFGEAGLPVPAGV--AAVLADAVRRNGYGPVAGSAEA 62 Query: 73 KNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVIIPTPYWVSYPEQVK 132 + + A F R + + P Q++ G+K L+ L +L +V++P P WVSY Q Sbjct: 63 REAAAGWFTR-RGLPTGPEQVLFAPGSKALLFAL---VLALPGDVVLPRPSWVSYAAQSA 118 Query: 133 LAGGKPVYVEGLEENHFKISPEQLKNAITEKTKA-------IVINSPSNPTGVMYTEEEL 185 LAG + + V PE+L+ A+ E+ +A +V+ P NPTG + E++ Sbjct: 119 LAGKRTIGVPIPAGAGGVPDPERLEGAL-ERARAEGAEPGVLVLTVPDNPTGTVARAEDV 177 Query: 186 SALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSHSMTGWR 245 A+ + H + +V+DEIY +L + ++ + D L E+TV+ +G+SKS ++ GWR Sbjct: 178 RAVCGIAERHGLAVVADEIYAELVHDADAARALPRAVDHLPERTVVTSGLSKSMALGGWR 237 Query: 246 IGYA-----AGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHRL 300 IG+A A E + + +AS S+ + Q A P E L + A RL Sbjct: 238 IGFARLPEGAWGERLRGELVGVASEIWSSLAAPMQAVAARVLEDPPEVLAHIAAA--RRL 295 Query: 301 NTIYAKLIE----IPGFSCVKPEGAFYLFPN---AKEAAQSCGFKDVDEFVKALLEEEKV 353 + A+ + G C PE FYL+P+ +E + G + E ALLE V Sbjct: 296 HGAVARAVHAEFAAAGAVCRAPEAGFYLYPDFEPVRERLAARGVRSGAELAAALLERYGV 355 Query: 354 AIVPGSGFG-SPENVRLSYATSLDLLEEAIER 384 ++ G+ FG + +R ATSL E ER Sbjct: 356 GVLAGAAFGDAAAGLRARVATSLLYGETEAER 387 Lambda K H 0.313 0.131 0.370 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: 376 Number of extensions: 17 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: 393 Length of database: 419 Length adjustment: 31 Effective length of query: 362 Effective length of database: 388 Effective search space: 140456 Effective search space used: 140456 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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