Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 3608394 Dshi_1794 aminotransferase class I and II (RefSeq)
Query= BRENDA::Q8YY14 (398 letters) >FitnessBrowser__Dino:3608394 Length = 393 Score = 155 bits (391), Expect = 2e-42 Identities = 110/354 (31%), Positives = 167/354 (47%), Gaps = 18/354 (5%) Query: 40 SPPPEAIE--LLPRFLADPANNLYKAVEGIPPLLNALTEKLSTFNNIEITTDNCIVVTAG 97 +PPP A+ + DP +LY V G+P L L +++ + + I +T+G Sbjct: 45 APPPPALRAAMAAALEEDPGTHLYGPVLGLPELRAELAAQMTARYGGTVA-EGQIAITSG 103 Query: 98 SNMAFMNAILAITSPGDEIILNTPYYFNHEMAITMAGCRAVLVETDENYQLCPEAIAQAI 157 N AF I + PGD +IL P+YFNH+M + M+G A ++T ++ PEA A I Sbjct: 104 CNQAFAAVIATLAGPGDNVILPVPWYFNHQMWLQMSGVAARALDTGDSLLPDPEAAAALI 163 Query: 158 TPKTRAVVTISPNNPTGVVYCEDLLRNVNQICANYGIYHISDEAYEYF-TYDGVKHVSPA 216 +TRA+V +SPNNP GV Y DLL + G+ I DE Y F + G H A Sbjct: 164 DARTRAIVLVSPNNPGGVEYPADLLAAFRDLARRRGLALILDETYRDFDSRAGAPHGLLA 223 Query: 217 SFAGSSEYTISLYSLSKAYGFASWRIGYMVIPKHLLVAIKKVQDTILICPPVVSQYAALG 276 E ISLYS SKAY R+G + L ++K DT+ IC P + Q AAL Sbjct: 224 D-PDWDETVISLYSFSKAYRLTGHRVGAVACAPDRLAQVEKFLDTVQICAPQLGQRAALW 282 Query: 277 ALQAKPEYLQDHIGALAQPAVGIAQVRQIVFDYLKQLQGLCNITPADGAFYVFLKVHTQI 336 L+ +L D + + + F L+ + L GA++ + + I Sbjct: 283 GLR----HLSDWLAGERAEILARRAAMEAAFQGLRDWELL-----GCGAYFGYARHRLGI 333 Query: 337 DAFALVKQLIQEYKVAVIPGTTFGME----NGCYLRVAYGALQKDTVKEGIERL 386 + AL ++++ E V +PGT F + G +R A+ + D + +RL Sbjct: 334 PSDALAERMVSEIGVLALPGTMFAPQGAARGGREMRFAFANIDADGIAALADRL 387 Lambda K H 0.320 0.136 0.398 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: 377 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 398 Length of database: 393 Length adjustment: 31 Effective length of query: 367 Effective length of database: 362 Effective search space: 132854 Effective search space used: 132854 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 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