Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate GFF3329 HP15_3271 aspartate aminotransferase
Query= CharProtDB::CH_017144 (393 letters) >FitnessBrowser__Marino:GFF3329 Length = 431 Score = 177 bits (450), Expect = 4e-49 Identities = 126/374 (33%), Positives = 203/374 (54%), Gaps = 23/374 (6%) Query: 7 VASLTPSATLAITEKAKELKAAGHDVIGLGAGEPDFNTPQHILDAAIKAMNEGHTKYTPS 66 V + PSATL I E + LK+ G D+I LG G+ F P +++A + +E Y P Sbjct: 15 VRGIQPSATLRINELSNHLKSEGKDIIKLGLGQSPFPVPDRVVEALKEHAHE--KDYLPV 72 Query: 67 GGLPALKEEIIKKFARDQGLDYEPAEVIVCVGAKHALYTLFQVLLDEGDEVIIPTPYWVS 126 GL L+E I R + + +V++ G+K L+ L L GD ++IP P WVS Sbjct: 73 KGLKGLREAIAGYIRRSERMHCTWEDVLIGPGSKELLFML--QLAYYGD-LLIPRPSWVS 129 Query: 127 YPEQVKLAGGVPVYVEGLEQNHFKITPEQLK---QAITPRTKAVIINSPSNPTGMIYTAE 183 Y Q ++ G ++ +N++++T E+L + R + +I+N PSNPTG YT + Sbjct: 130 YAPQARIIGRSVHWLPTHAENNWQLTAEELDIICRDDPSRPRILILNYPSNPTGCTYTDD 189 Query: 184 ELKALGEVCLAHGVLIVSDEIYEKLTYGGAKHVSIAELSPELKAQTVIINGVSKSHSMTG 243 +L A+ V + ++++SDEIY ++ + G +H SIA PE T+I G+SK G Sbjct: 190 QLLAIANVARKYRLILLSDEIYGEVHFEG-RHKSIARYYPE---GTIISTGLSKWAGAGG 245 Query: 244 WRIGYAAGPKD---IIKAMTDLASHSTSNPTSIAQYAAIAAYSGPQEPVEQMRQAFEQRL 300 WR+G P++ + AM +AS + + ++ Q+AAIAA++G + E ++Q+ + L Sbjct: 246 WRLGTFIFPRELRPLQDAMAIIASETYTATSAPIQHAAIAAFNGGDDIDEYLKQS-RRVL 304 Query: 301 NIIYD---KLVQIPGFTCVKPQGAFYLFPN---AREAAAMAGCRTVDEFVAALLEEAKVA 354 ++ + + + G KP+GAFYLFP+ RE A +T F ALLE VA Sbjct: 305 KVVGEYMHRRLSDMGAVVQKPEGAFYLFPDFSGFREQLASKDIKTSQAFCQALLENTGVA 364 Query: 355 LVPGSGFG-APDNV 367 ++P S FG PD++ Sbjct: 365 ILPASDFGFVPDHL 378 Lambda K H 0.316 0.133 0.381 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: 349 Number of extensions: 16 Number of successful extensions: 7 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: 431 Length adjustment: 31 Effective length of query: 362 Effective length of database: 400 Effective search space: 144800 Effective search space used: 144800 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 (21.6 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