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 WP_090443468.1 BLS63_RS09835 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q02635 (400 letters) >NCBI__GCF_900100495.1:WP_090443468.1 Length = 404 Score = 431 bits (1107), Expect = e-125 Identities = 211/393 (53%), Positives = 277/393 (70%) Query: 8 LSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPV 67 L+ +PSAT + + +A+G +I L AGEPDFDTP +I++AAI AI+ G T+YT V Sbjct: 12 LAAAQPSATYRIIDRVAARRAQGTSIISLCAGEPDFDTPRHIRQAAIAAIEAGHTRYTQV 71 Query: 68 SGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVS 127 +G+ LREA+A K++ EN L + T V +GGKQ+++NA TLN DEV+IPAPYWVS Sbjct: 72 AGLRALREAVAAKYRDENGLAVSWEDTQVSSGGKQVIYNALAGTLNESDEVIIPAPYWVS 131 Query: 128 YPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELK 187 YPEMV LCGG V ++ FKL A+ L +I P T+W + NSPSNP+GA YS EEL+ Sbjct: 132 YPEMVQLCGGRSRIVTCGADSGFKLTAQALRESIGPDTRWLILNSPSNPTGAVYSREELR 191 Query: 188 ALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWR 247 AL +VL++ P V +L+DD+YEHL + F T +VEP L ERTLTMNGVSKAYAMTGWR Sbjct: 192 ALAEVLLEQPQVLILSDDIYEHLIFDGRSFHTLAQVEPRLAERTLTMNGVSKAYAMTGWR 251 Query: 248 IGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVS 307 IG+A GP L++AM+ +QGQQTSGA SI+Q AAV AL GP+DFI ++E+FQ RRD +V+ Sbjct: 252 IGFATGPRWLLEAMEKLQGQQTSGACSISQHAAVAALGGPKDFIHESREVFQRRRDFMVA 311 Query: 308 MLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSA 367 +LN G+ C PEGAFY + C+ L+GK +P G+ + +DED LL+ VAVV GSA Sbjct: 312 LLNDTPGLHCALPEGAFYAFADCSALLGKVSPGGRGLISDEDLAHALLDEANVAVVPGSA 371 Query: 368 FGLGPNFRISYATSEALLEEACRRIQRFCAACR 400 FGL RI+YA +A L++AC IQ+FC R Sbjct: 372 FGLAGYIRIAYALDDASLKKACEAIQQFCRNAR 404 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: 462 Number of extensions: 14 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: 404 Length adjustment: 31 Effective length of query: 369 Effective length of database: 373 Effective search space: 137637 Effective search space used: 137637 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 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