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_012334619.1 M446_RS23585 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q02635 (400 letters) >NCBI__GCF_000019365.1:WP_012334619.1 Length = 392 Score = 248 bits (632), Expect = 3e-70 Identities = 147/396 (37%), Positives = 212/396 (53%), Gaps = 13/396 (3%) Query: 7 ALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTP 66 A +R+ AV +A L GRDVI LG G+PD TP ++ +AAI A+ G YTP Sbjct: 7 AFARIGEENAFAVLARATALAQAGRDVINLGIGQPDMPTPPHVVEAAIKALRDGHHGYTP 66 Query: 67 VSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWV 126 +GI LREA+A+ R ++ + ++ GGK +F A + PG E++ P P + Sbjct: 67 ATGILPLREAVARDLHRRLEVEVSPDSVMIVPGGKVTMFAAILMFGEPGAEILYPDPGFP 126 Query: 127 SYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEEL 186 Y M+ G TPV +P R+ N F AE+ I+P+T+ + NSP+NP+G E+ Sbjct: 127 IYRSMIEFTGATPVPIPIREANGFAFSAEETLALISPRTRLLIVNSPANPTGGVTPKAEI 186 Query: 187 KALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGW 246 L L HP V VL+D++Y +TY R T + P + +R + ++G SK YAMTGW Sbjct: 187 DRLVAGLAAHPDVAVLSDEIYGTMTYDGARHHT-LLAYPEIRDRLIYLDGASKTYAMTGW 245 Query: 247 RIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVV 306 R+G++ P L +A + S + QWA + AL+GPQD + F RR LVV Sbjct: 246 RLGWSVWPAPLYEAARKLAVNSFSCVNAATQWAGIAALDGPQDAVAAMMAEFDRRRLLVV 305 Query: 307 SMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGS 366 LN+ G+SC TP+GAFY +P+ I +T K + S LLE G+A + G Sbjct: 306 EGLNRLPGVSCITPKGAFYAFPN----IARTGWKAKAL------ASALLEEAGIAAIGGP 355 Query: 367 AFGL-GPNF-RISYATSEALLEEACRRIQRFCAACR 400 FG+ G + R+SYA S + A R+ F AA R Sbjct: 356 DFGVHGEGYLRLSYANSAENIARALERMGGFLAANR 391 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: 437 Number of extensions: 14 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: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 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