Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 202 bits (513), Expect = 3e-56 Identities = 124/383 (32%), Positives = 195/383 (50%), Gaps = 19/383 (4%) Query: 19 VSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIA 78 + A + ++G D+I L G+PDF TP I AA+ A+ G+T YT + G P LREAIA Sbjct: 20 IHHAAFQAASQGEDIIILSVGDPDFATPSFITDAAVSALREGDTHYTEIPGRPALREAIA 79 Query: 79 KKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGT 138 ++ + +A I G + LF + L GDEV++ P +V+Y + G T Sbjct: 80 ARYSKTLARALSAENVITVAGAQNALFVTSLCLLQAGDEVLVLDPMYVTYEATLKASGAT 139 Query: 139 PVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPH 198 V VP E+ F+L A+ L AITP+T+ F++P+NP+G + +EL+A+ D+ + Sbjct: 140 LVRVPCSPESGFRLDAQLLGAAITPRTRAIFFSNPNNPTGVVLNLQELQAIADLAIAR-D 198 Query: 199 VWVLTDDMYEHLTY-GDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHL 257 +WV+ D++YE L + G++ + PG+ ER + + +SK++AMTGWRIG+ + Sbjct: 199 LWVVVDEVYESLVFDGEYHSLAAL---PGMAERCVVIGSLSKSHAMTGWRIGWIIATPQM 255 Query: 258 IKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISC 317 + + + G AA A+ D +EI++ RRDLV++ L+ GI Sbjct: 256 VAHAETLVLSMLYGLPGFVMEAATAAVLAHDDVTQGMREIYRRRRDLVMAGLSACPGIKV 315 Query: 318 PTPEGAFYVYPSCAGL-IGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFGLGPN--F 374 P+ +V G +G DF L GV+V+ +AFG Sbjct: 316 QAPQAGMFVLVDVRGTGLGSL-----------DFAWRLFREAGVSVLDAAAFGAPAQGFV 364 Query: 375 RISYATSEALLEEACRRIQRFCA 397 R+S+ E L EAC+RI F A Sbjct: 365 RLSFTLGEERLSEACQRIAHFVA 387 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: 570 Number of extensions: 27 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: 400 Length of database: 664 Length adjustment: 35 Effective length of query: 365 Effective length of database: 629 Effective search space: 229585 Effective search space used: 229585 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: 52 (24.6 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