Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate 6937541 Sama_1697 aminotransferase AlaT (RefSeq)
Query= CharProtDB::CH_017144 (393 letters) >FitnessBrowser__SB2B:6937541 Length = 404 Score = 164 bits (416), Expect = 3e-45 Identities = 115/386 (29%), Positives = 192/386 (49%), Gaps = 19/386 (4%) Query: 18 ITEKAKELKAAGHDVIGLGAGEP---DFNTPQHILDAAIKAMNEGHTKYTPSGGLPALKE 74 + ++A+ L+ GH ++ L G P F P+ I+ I + Y S GL + ++ Sbjct: 21 VHKEARRLEDEGHRILKLNIGNPAPFGFEAPEEIVRDVILNLPSAQG-YCESKGLFSARK 79 Query: 75 EIIKKFARDQGLDYEPAEVIVCVGAKHALYTLFQVLLDEGDEVIIPTPYWVSYPEQVKLA 134 I++ + + +V + G + Q LL+ DEV+IP+P + + LA Sbjct: 80 AIVQHYQSQGIFGVDIEDVYIGNGVSELIVMALQGLLNGDDEVLIPSPDYPLWTAAANLA 139 Query: 135 GGVPVYVEGLEQNHFKITPEQLKQAITPRTKAVIINSPSNPTGMIYTAEELKALGEVCLA 194 GG V+ E++ + + +K I+PRT+A++I +P+NPTG +Y+ E L + E+C Sbjct: 140 GGKAVHYRCDEESDWFPCLDDIKAKISPRTRAIVIINPNNPTGAVYSRELLLEIIELCRQ 199 Query: 195 HGVLIVSDEIYEKLTYGGAKHVSIAELSPELKAQTVIINGVSKSHSMTGWRIGY------ 248 H +++ +DEIY+K+ Y A H+ A LS ++ TV NG+SK++ G+R+G+ Sbjct: 200 HSLILFADEIYDKILYDDAVHIPAAGLSDDI--LTVTFNGLSKAYRAAGFRVGWMMLSGN 257 Query: 249 AAGPKDIIKAMTDLASH--STSNPTSIAQYAAIAAYSGPQEPVEQMRQAFEQRLNIIYDK 306 K I+ + LAS + P A A+ Y E + + QR + Y+ Sbjct: 258 LKAAKSYIEGLDMLASMRLCANVPNQHAVQTALGGYQSINELILPKGRLSVQR-DTCYEY 316 Query: 307 LVQIPGFTCVKPQGAFYLFPNAREAAAMAGCRTVDEFVAALLEEAKVALVPGSGFG--AP 364 L IPG +C KP+GA Y FP + R + V LL+E K+ LV GS F P Sbjct: 317 LNAIPGVSCKKPKGALYAFP--KLDPKRFNLRDDERLVLDLLKEKKILLVQGSAFNWPEP 374 Query: 365 DNVRLSYATSLDALETAVERIHRFME 390 D++R+ + + LE A+ F+E Sbjct: 375 DHLRVVFLPHKEDLEKALGAFGEFLE 400 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: 372 Number of extensions: 23 Number of successful extensions: 4 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: 404 Length adjustment: 31 Effective length of query: 362 Effective length of database: 373 Effective search space: 135026 Effective search space used: 135026 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