Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_106709221.1 CU102_RS01735 aminotransferase
Query= BRENDA::O69689 (435 letters) >NCBI__GCF_003010955.1:WP_106709221.1 Length = 432 Score = 447 bits (1149), Expect = e-130 Identities = 214/416 (51%), Positives = 291/416 (69%), Gaps = 2/416 (0%) Query: 6 LSPQELAALHARHQQDYAALQGMKLALDLTRGKPSAEQLDLSNQLLSLPGD-DYRDPEGT 64 LS ++L AL R +Y A + L +D+TRGKPS EQLDL+N +L+LPG+ D+ G Sbjct: 7 LSAEDLRALRNRVLGEYEAFRARGLQIDMTRGKPSPEQLDLANGMLALPGNGDHFTEAGE 66 Query: 65 DTRNYGGQHGLPGLRAIFAELLGIAVPNLIAGNNSSLELMHDIVAFSMLYGGVDSPRPWI 124 D RNYGG GLP +RA+FA ++G ++ G+NSSL LMHD + +S+ G + PW Sbjct: 67 DARNYGGLQGLPEVRALFAPMMGAPAERVVVGDNSSLALMHDCLVWSLFKGVSNEMEPWS 126 Query: 125 QEQDGIKFLCPVPGYDRHFAITETMGIEMIPIPMLQDGPDVDLIEELVAVDPAIKGMWTV 184 Q+ F+CPVPGYDRHFAI E GI M+P+P+ GPD+D++EEL A DP +KGMW V Sbjct: 127 QQSGTPAFICPVPGYDRHFAICEEYGIRMLPVPLTGHGPDMDIVEELAA-DPDVKGMWCV 185 Query: 185 PVFGNPSGVTYSWETVRRLVQMRTAAPDFRLFWDNAYAVHTLTLDFPRQVDVLGLAAKAG 244 P + NPSG YS E + RL MRT APDFRLFWDNAYAVH LT ++L L A+AG Sbjct: 186 PKYSNPSGEIYSTEVIERLAAMRTGAPDFRLFWDNAYAVHHLTPQRHEIANILELCAQAG 245 Query: 245 NPNRPYVFASTSKITFAGGGVSFFGGSLGNIAWYLQYAGKKSIGPDKVNQLRHLRFFGDA 304 NP+R +VFASTSK+T AG G++ F S N+ WYL AGK++IGPDK+NQ+RH+RF + Sbjct: 246 NPDRAFVFASTSKVTLAGAGLALFASSAANVKWYLARAGKRTIGPDKLNQIRHVRFLKNI 305 Query: 305 DGVRLHMLRHQQILAPKFALVAEVLDQRLSESKIASWTEPKGGYFISLDVLPGTARRTVA 364 +G+ HM H+ ++APKF V + LD+RLS + IA WT+P+GGYFI +D + GTA+ V Sbjct: 306 EGLHEHMEAHRALIAPKFDAVIDALDKRLSGTGIAHWTKPEGGYFICVDGMEGTAKHVVD 365 Query: 365 LAKDVGIAVTEAGASFPYRKDPDDKNIRIAPSFPSVPDLRNAVDGLATCALLAATE 420 LA+ G+ +T AGA+ PY +DP D+ +R+AP++PS+ +++ A +G+A C LLAA E Sbjct: 366 LARQAGVVLTPAGATSPYGRDPHDRTLRLAPTYPSLREVQQASEGIALCILLAALE 421 Lambda K H 0.320 0.138 0.415 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: 577 Number of extensions: 24 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: 435 Length of database: 432 Length adjustment: 32 Effective length of query: 403 Effective length of database: 400 Effective search space: 161200 Effective search space used: 161200 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: 51 (24.3 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