Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF1734 Psest_1772 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__psRCH2:GFF1734 Length = 403 Score = 150 bits (378), Expect = 8e-41 Identities = 120/395 (30%), Positives = 191/395 (48%), Gaps = 35/395 (8%) Query: 19 VSQKARELKAKGRDVIGLGAGEP---DFDTPDNIKKAAIDAIDRGETKYTPVSGIPELRE 75 V + A+ L+ +G ++ L G P F+ P+ I + I + + Y+ G+ R+ Sbjct: 20 VLKHAKRLEEEGHRILKLNIGNPAPFGFEAPEEILQDVIRNLPTAQG-YSDSKGLFSARK 78 Query: 76 AIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALC 135 AI + ++++ + +G G +++ + A LN GDEV+IPAP + + V+L Sbjct: 79 AIMQYYQQKQVEGVSIEDIYLGNGVSELIVMSMQALLNNGDEVLIPAPDYPLWTAAVSLA 138 Query: 136 GGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMK 195 GG PV ++ N+ D+ ITP TK V +P+NP+GA Y E L+ + ++ + Sbjct: 139 GGKPVHYLCDEQANWWPDLADIKAKITPNTKALVLINPNNPTGAVYPKEVLEGMVELARQ 198 Query: 196 HPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAA--G 253 H V + +D++Y+ + Y D + + P + LT NG+SK+Y + G+R G+ A G Sbjct: 199 HKLV-LFSDEIYDKILYDDAVHISTASLAPDVL--CLTFNGLSKSYRVAGFRSGWVAISG 255 Query: 254 PLHLIKAMDMIQGQQTSGAASI-----AQWAAVEALNGPQ---DFI---GRNKEIFQGRR 302 P H KA I+G + AQ A AL G Q D + GR E +R Sbjct: 256 PKH--KAQSYIEGLDILANMRLCANVPAQHAIQTALGGYQSINDLVLPPGRLLE----QR 309 Query: 303 DLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAV 362 + +LN GISC P GA Y +P + P I DE FV +LL +E + + Sbjct: 310 NRTWELLNDIPGISCVKPMGALYAFP-------RIDPKICPIHNDEKFVLDLLLSEKLLI 362 Query: 363 VHGSAFG--LGPNFRISYATSEALLEEACRRIQRF 395 V G+AF +FR+ LE+A RI F Sbjct: 363 VQGTAFNWPWPDHFRVVTLPRVDDLEQAIGRIGNF 397 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: 356 Number of extensions: 19 Number of successful extensions: 4 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: 403 Length adjustment: 31 Effective length of query: 369 Effective length of database: 372 Effective search space: 137268 Effective search space used: 137268 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