Align Aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_012283547.1 HM1_RS11430 aminotransferase class V-fold PLP-dependent enzyme
Query= curated2:Q9V0L2 (389 letters) >NCBI__GCF_000019165.1:WP_012283547.1 Length = 395 Score = 338 bits (866), Expect = 2e-97 Identities = 172/376 (45%), Positives = 246/376 (65%), Gaps = 3/376 (0%) Query: 12 PSEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDMGLTHYGPNIGLPELREA 71 PS IR+ FD+ A K VISLG+GEPDF TP H++E AL+ G T Y N G PELR+ Sbjct: 18 PSGIRRFFDLVANTKGVISLGVGEPDFVTPWHVRESCFYALERGYTMYTSNFGTPELRKE 77 Query: 72 IAEKLKKQNNIEADPNKEIMVLVGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAPAVILA 131 I +++ ++ DP E++V VGA++A + + L G+EVL+P P++VSY+P V +A Sbjct: 78 ITRFIQRSYGVDYDPLSEVLVTVGASEAVDLAMRMLLCPGDEVLVPEPSYVSYSPTVTMA 137 Query: 132 GGKPVEVPTYEENEFRLNVDELKKYVTEKTKALIINSPCNPTGSVLKKKDLEEIADFAVE 191 GG V VPTY +++F+L V+ L+K V+ +TK L++ P NPTG+++ + +LE IA FA E Sbjct: 138 GGVAVAVPTYVKDDFQLTVEALEKKVSPRTKMLVLCYPNNPTGAIMTRPELEAIARFAEE 197 Query: 192 HDLIVISDEVYEHFIYDDVKHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAPSWI 251 DLIV++DE+Y Y++ +H A L GM +RT+ +NG SK+ AMTGWR+G+V Sbjct: 198 RDLIVLADEIYAELTYEE-QHVCFAGLPGMRDRTVLINGLSKSHAMTGWRIGYVCGNKDF 256 Query: 252 IEKMVKFQMYNATCPVTFIQYAAAKALRDERSWKAVEEMRKEYDRRRKLVWKRLNEMGLP 311 I +M K Y C Q AA +ALR+ K+ M +YD+RR+ V R N+MGL Sbjct: 257 IAQMTKIHQYTILCAPIMGQMAALEALRNGDLEKS--RMVNQYDQRRRFVVARFNQMGLT 314 Query: 312 TVKPKGAFYIFPRIKDTGLTSKEFSELMLMEAKVAVVPGSAFGKAGEGYVRISYATAYEK 371 P+GAFY FP I TGL+S +F E +L E KVAVVPG+AFG +GEG++R+SYA++ Sbjct: 315 CFNPRGAFYAFPSITATGLSSDDFCEQLLAEEKVAVVPGTAFGASGEGFIRVSYASSMAN 374 Query: 372 LEEAMDRMEKVLREKK 387 L A+DR+E ++ K Sbjct: 375 LTTALDRIEAFVQRCK 390 Lambda K H 0.318 0.135 0.389 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: 406 Number of extensions: 11 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: 389 Length of database: 395 Length adjustment: 31 Effective length of query: 358 Effective length of database: 364 Effective search space: 130312 Effective search space used: 130312 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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