Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF3717 PS417_19025 aspartate aminotransferase
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__WCS417:GFF3717 Length = 401 Score = 360 bits (924), Expect = e-104 Identities = 175/398 (43%), Positives = 253/398 (63%) Query: 3 FLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGET 62 FL+D + + PS +IA + EL+A+GRD++ GEPDFDTP +I AA A+ G+T Sbjct: 4 FLSDRVLGIAPSPSIAANALVTELRAQGRDIVNFTVGEPDFDTPAHILAAASQAMHNGDT 63 Query: 63 KYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPA 122 YT +G LR+AI K +++N+L Y + + G GGK ++++A ATLN GDEV++ Sbjct: 64 HYTSTTGTLALRQAICLKLQQDNDLAYGLDEVVAGCGGKHVIYHALAATLNRGDEVIVHT 123 Query: 123 PYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYS 182 PYWVSYP++ L TPV +P + FKL + L++AIT +TKW + NSP+NPSGA Y+ Sbjct: 124 PYWVSYPDIARLNDATPVIIPGDESLGFKLSPDALEQAITARTKWVILNSPNNPSGAVYN 183 Query: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242 EL AL VL +HPHV ++ D++YEH YG R + P L RTL +NG SK YA Sbjct: 184 ETELLALAQVLRRHPHVLIMADEIYEHFIYGRARHVPLTRLAPDLKPRTLIVNGASKGYA 243 Query: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRR 302 MTGWR+G+ AGP LI A+ + Q T+ +S++Q AAV A G Q I +E +Q RR Sbjct: 244 MTGWRLGFGAGPAWLIAAIAKLLSQTTTCPSSLSQAAAVAAFTGDQAPIAAMREEYQQRR 303 Query: 303 DLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAV 362 ++++L G+SC P+GAFYV+ + +GL+GK P G +++D V LL G+A Sbjct: 304 ARMLALLADIPGLSCTPPDGAFYVFANVSGLMGKLTPQGDRLDSDTQLVDYLLRDYGLAT 363 Query: 363 VHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400 V G+A+G+ P R+S+A+S ++EE CRR++ C R Sbjct: 364 VSGAAYGMSPYVRLSFASSSEVIEEGCRRLKDACRDLR 401 Lambda K H 0.318 0.134 0.402 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: 438 Number of extensions: 16 Number of successful extensions: 1 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: 400 Length of database: 401 Length adjustment: 31 Effective length of query: 369 Effective length of database: 370 Effective search space: 136530 Effective search space used: 136530 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 Aug 03 2021. The underlying query database was built on Aug 03 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