Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_012592214.1 MSIL_RS16485 aminotransferase
Query= BRENDA::O69689 (435 letters) >NCBI__GCF_000021745.1:WP_012592214.1 Length = 431 Score = 446 bits (1146), Expect = e-130 Identities = 221/429 (51%), Positives = 294/429 (68%), Gaps = 3/429 (0%) Query: 4 DSLSPQELAALHARHQQDYAALQGMKLALDLTRGKPSAEQLDLSNQLLSLPGD-DYRDPE 62 D LS ELAAL A Q +Y A + L LD+TRGKP+ +QLDL+N +LSL G+ DYR Sbjct: 5 DQLSKAELAALRASVQANYDAFRAQGLKLDMTRGKPAPDQLDLANAMLSLMGNADYRSEA 64 Query: 63 GTDTRNYGGQHGLPGLRAIFAELLGIAVPNLIAGNNSSLELMHDIVAFSMLYGGVDSPRP 122 G D RNYG GL RA+ A +LG ++ G+NSSL LMHD + +++ G S RP Sbjct: 65 GEDARNYGNLQGLAEARALIAPILGAPPEQIVVGDNSSLALMHDSLVYALTKGVPGSARP 124 Query: 123 WIQEQDGIKFLCPVPGYDRHFAITETMGIEMIPIPMLQDGPDVDLIEELVAVDPAIKGMW 182 W +E+ + F+CP PGYDRHFAI E G+ M+P+ M +GPD++ +E L A DPA+KG+W Sbjct: 125 WAKEES-VAFICPAPGYDRHFAICEEYGVRMLPVRMTGEGPDMEEVERLAA-DPAVKGIW 182 Query: 183 TVPVFGNPSGVTYSWETVRRLVQMRTAAPDFRLFWDNAYAVHTLTLDFPRQVDVLGLAAK 242 VP + NP+G YS TV RL MRT A DFR+FWD+AY VH LT ++L A+ Sbjct: 183 AVPKYSNPTGDIYSDATVARLAAMRTGARDFRIFWDDAYCVHHLTAQRNAVANILEECAR 242 Query: 243 AGNPNRPYVFASTSKITFAGGGVSFFGGSLGNIAWYLQYAGKKSIGPDKVNQLRHLRFFG 302 AGN +R ++FASTSKIT AG G++FF S N+ WYL A K+SIGPDK+NQLRH+RF Sbjct: 243 AGNQDRAFIFASTSKITLAGAGLAFFASSPANVKWYLSSASKRSIGPDKLNQLRHVRFLR 302 Query: 303 DADGVRLHMLRHQQILAPKFALVAEVLDQRLSESKIASWTEPKGGYFISLDVLPGTARRT 362 DA+G+ HM H+ ++APKFA V E LD+ L+ + A+W+ P+GGYFIS++ GTARR Sbjct: 303 DAEGINAHMDAHRALIAPKFAAVIEALDRHLAGTGAANWSVPQGGYFISVEASAGTARRV 362 Query: 363 VALAKDVGIAVTEAGASFPYRKDPDDKNIRIAPSFPSVPDLRNAVDGLATCALLAATETL 422 V LAK G+A+T AGA++PY KDPDD N+R+AP+FP++ ++R A +G+A C LLAA E Sbjct: 363 VELAKAAGVALTPAGATWPYGKDPDDSNLRLAPTFPTLAEVRAASEGIALCILLAALEAR 422 Query: 423 LNQGLASSA 431 Q S+A Sbjct: 423 TAQAAESAA 431 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: 523 Number of extensions: 23 Number of successful extensions: 5 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: 431 Length adjustment: 32 Effective length of query: 403 Effective length of database: 399 Effective search space: 160797 Effective search space used: 160797 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 Apr 10 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