Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate PP_1872 PP_1872 glutamate-pyruvate aminotransferase
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__Putida:PP_1872 Length = 403 Score = 148 bits (373), Expect = 3e-40 Identities = 119/394 (30%), Positives = 193/394 (48%), Gaps = 33/394 (8%) Query: 19 VSQKARELKAKGRDVIGLGAGEP---DFDTPDNIKKAAIDAIDRGETKYTPVSGIPELRE 75 V + A+ L+ +G ++ L G P F+ PD I + I + + Y+ G+ R+ Sbjct: 20 VLKHAKRLEEEGHRILKLNIGNPAPFGFEAPDEILQDVIRNLPTAQG-YSDSKGLFSARK 78 Query: 76 AIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALC 135 A+ + ++++ T +G G +++ + A LN GDEV+IPAP + + V+L Sbjct: 79 AVMQYCQQKDIEGVTIEDIYLGNGVSELIVMSMQALLNNGDEVLIPAPDYPLWTAAVSLA 138 Query: 136 GGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMK 195 GG PV ++ ++ ED+ ITP TK V +P+NP+GA YS E L + ++ + Sbjct: 139 GGKPVHYLCDEQADWFPDLEDIKAKITPNTKALVIINPNNPTGAVYSKELLLGMLELARQ 198 Query: 196 HPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGY--AAG 253 H ++ V +D++Y+ + Y + + + P L LT NG+SK+Y + G+R G+ +G Sbjct: 199 H-NLVVFSDEIYDKILYDEAVHISTASLAPDLL--CLTFNGLSKSYRVAGFRSGWLIISG 255 Query: 254 PLH----LIKAMDMIQGQQTSGAASIAQWAAVEALNGPQ---DFI---GRNKEIFQGRRD 303 P H I+ +DM+ + A AQ A AL G Q D + GR E +R+ Sbjct: 256 PKHHAHSYIEGIDMLANMRLC-ANVPAQHAIQTALGGYQSINDLVLPPGRLLE----QRN 310 Query: 304 LVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVV 363 +LN G+SC P GA Y +P + P I DE F +LL +E + +V Sbjct: 311 RTYELLNDIPGVSCVKPMGALYAFP-------RIDPKVCPILNDEKFALDLLLSEKLLIV 363 Query: 364 HGSAFG--LGPNFRISYATSEALLEEACRRIQRF 395 G+AF +FR+ LE A RI F Sbjct: 364 QGTAFNWPWPDHFRVVTLPRVDDLEAAIGRIGNF 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: 364 Number of extensions: 21 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 Apr 09 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