Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_017548955.1 C792_RS0108030 pyridoxal phosphate-dependent aminotransferase
Query= CharProtDB::CH_004890 (393 letters) >NCBI__GCF_000330705.1:WP_017548955.1 Length = 395 Score = 452 bits (1163), Expect = e-132 Identities = 218/389 (56%), Positives = 285/389 (73%), Gaps = 1/389 (0%) Query: 1 MKLAKRVSALTPSTTLAITAKAKELKAAGHDVIGLGAGEPDFNTPQHIIDAAVRSMNEGH 60 M+++ R+ +TPS TLAITAK+++LKA G DVIGLGAGEPDFNTP IID A S+ G Sbjct: 1 MQISDRIKNVTPSQTLAITAKSRDLKAQGVDVIGLGAGEPDFNTPDEIIDKAYESLKAGK 60 Query: 61 TKYTPSGGLAELKNSIAEKFKRDQNIEYKPSQIIVCTGAKHALYTLFQVILDEEDEVIIP 120 TKYT + G+ ELK++I K ++D + Y+PS++ V GAKH LY LFQ L+ DEVIIP Sbjct: 61 TKYTAAAGIPELKSAIINKMEKDHGLVYEPSEVFVGNGAKHVLYNLFQATLNPGDEVIIP 120 Query: 121 TPYWVSYPEQVKLAGGKPVYVEGLEENHFKISPEQLKNAITEKTKAIVINSPSNPTGVMY 180 PYWVSY EQVKLAGG PV + E FK++PE + +T+KT+ +++NSPSNP+G++Y Sbjct: 121 VPYWVSYTEQVKLAGGNPVIMPTDESTSFKVTPEIIDGFLTDKTRMLLLNSPSNPSGMVY 180 Query: 181 TEEELSALGEVCLEHDILIVSDEIYEKLTYGGKKHVSIAQLSDRLKEQTVIINGVSKSHS 240 T EEL AL E D+++V+DEIYE L Y +H+SIA LS+R+KE T +INGVSKSH+ Sbjct: 181 TREELEALAAYIEEKDLIVVADEIYETLVY-DSEHISIASLSNRMKENTFVINGVSKSHA 239 Query: 241 MTGWRIGYAAGSEDIIKAMTNLASHSTSNPTSIAQYGAIAAYNGPSEPLEEMREAFEHRL 300 MTGWRIGY G+ ++KAMT+L SHSTSNP + +Q+ AIAAY E F R Sbjct: 240 MTGWRIGYCCGNSGVVKAMTDLTSHSTSNPVTPSQWAAIAAYEMDDSFTREYNRTFHERR 299 Query: 301 NTIYAKLIEIPGFSCVKPEGAFYLFPNAKEAAQSCGFKDVDEFVKALLEEEKVAIVPGSG 360 + Y KL+EIP +C+KP+GAFYLFPN E A+ CGF VD FV A+LEE VA+VPGSG Sbjct: 300 DAAYEKLMEIPYITCIKPQGAFYLFPNFSECAERCGFDSVDAFVNAVLEEVYVAVVPGSG 359 Query: 361 FGSPENVRLSYATSLDLLEEAIERIKRFV 389 FGSP+N+RLSY+ S++ + EA+ERI++FV Sbjct: 360 FGSPDNIRLSYSLSIEDMNEALERIRKFV 388 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: 534 Number of extensions: 23 Number of successful extensions: 2 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: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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 Jul 26 2024. The underlying query database was built on Jul 25 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