Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate 5209443 Shew_1914 aminotransferase AlaT (RefSeq)
Query= CharProtDB::CH_004890 (393 letters) >FitnessBrowser__PV4:5209443 Length = 404 Score = 174 bits (440), Expect = 5e-48 Identities = 114/386 (29%), Positives = 199/386 (51%), Gaps = 19/386 (4%) Query: 21 KAKELKAAGHDVIGLGAGEP---DFNTPQHIIDAAVRSMNEGHTKYTPSGGLAELKNSIA 77 +A+ L+ GH ++ L G P F P+ I+ + ++ Y+ S GL + +I Sbjct: 24 EARRLEDEGHRILKLNIGNPAPFGFEAPEEIVRDVILNLPSAQG-YSESKGLFSARKAIV 82 Query: 78 EKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVIIPTPYWVSYPEQVKLAGGK 137 + ++ I + G + Q +L+ +DEV++P+P + + V L+GGK Sbjct: 83 QHYQSLGLFGVDIEDIYIGNGVSELIVMAMQGLLNSDDEVLVPSPDYPLWTAAVHLSGGK 142 Query: 138 PVYVEGLEENHFKISPEQLKNAITEKTKAIVINSPSNPTGVMYTEEELSALGEVCLEHDI 197 + EE+ + + +K+ I+ +T+ IV+ +P+NPTG +Y+ E L + E+C +HDI Sbjct: 143 AQHYRCDEESDWFPDLDDIKSKISSRTRGIVLINPNNPTGAVYSRELLLEIIELCRQHDI 202 Query: 198 LIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSHSMTGWRIGY------AAG 251 ++ +DEIY+K+ Y G H+ A LSD + TV NG+SKS+ G+R+G+ Sbjct: 203 ILFADEIYDKILYDGAVHIPAATLSDDI--LTVTFNGLSKSYRAAGFRVGWMMLSGNLKA 260 Query: 252 SEDIIKAMTNLASH--STSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHRLNTIYAKLIE 309 ++ I+ + LAS ++ P A A+ Y +E L + NT Y L + Sbjct: 261 AKSYIEGLDMLASMRLCSNVPNQHAIQTALGGYQSINE-LVAPEGRLTLQRNTCYELLNQ 319 Query: 310 IPGFSCVKPEGAFYLFPNAKEAAQSCGFKDVDEFVKALLEEEKVAIVPGSGFG--SPENV 367 IPG SC KP+GA Y FP K A+ +D + V LL+E+K+ +V G+ F P+++ Sbjct: 320 IPGVSCKKPKGALYAFP--KLDAKKFNLRDDERLVLDLLKEKKILLVQGTAFNWPEPDHL 377 Query: 368 RLSYATSLDLLEEAIERIKRFVEKHS 393 R+ + + L +A+ F+ +S Sbjct: 378 RVVFLPHKEDLHKALVEFGDFLTSYS 403 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: 398 Number of extensions: 19 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: 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 ( 7.2 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 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