Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_090442923.1 BLS63_RS08895 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_900100495.1:WP_090442923.1 Length = 382 Score = 190 bits (483), Expect = 5e-53 Identities = 128/358 (35%), Positives = 183/358 (51%), Gaps = 16/358 (4%) Query: 36 LTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSVTPE-ET 94 L+ G PDFD P+ ++EA R +A G +YAP G+P LRE +A K R G ++ P+ E Sbjct: 29 LSQGFPDFDGPQALREAVGRHIAAGHNQYAPMTGLPALREQVAAKIARCYGRALDPDGEV 88 Query: 95 IVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFVPDP 154 +T G QA+F QA++ PGDEVIV P + SY V AGG V V L GF D Sbjct: 89 TITPGATQAIFCAIQALVQPGDEVIVFDPCYDSYEPSVLLAGGRCVHVP-LALPGFAIDW 147 Query: 155 ERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYEGE 214 +R+ A++ RT+ +++NSP+NP+GA+ LE LA L + D YLVSDE+YEHL+++G Sbjct: 148 QRLADALSDRTRLIILNSPHNPSGALISPVELEQLAALIRDRDIYLVSDEVYEHLVFDGV 207 Query: 215 HFSPGRVAPE---HTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPDTIA 271 + E V+ K + +TGW+ GY P + + V + T Sbjct: 208 PHASVLAHEELYQRAFVVSSFGKTYHVTGWKTGYVVAPPALSAELRKVHQYVSFCGVTPL 267 Query: 272 QWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSPIA 331 QWA + + VE Y+ +RDL + L R +G ++ L D S I Sbjct: 268 QWALADFMAEHP---EHVEELPAFYQAKRDLFCDLLADSRFTFNRAAGTYFQLADYSAIR 324 Query: 332 PD--EVRAAERLL-EAGVAVVPGTDF-----AAFGHVRLSYATSEENLRKALERFARV 381 D +V AE L E GVA +P + F VR +A EE LR+A E+ + Sbjct: 325 ADLGDVAMAEWLTREHGVAAIPVSVFYQQPPKDLRLVRFCFAKREETLRQAAEKLCAI 382 Lambda K H 0.317 0.133 0.379 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: 345 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: 385 Length of database: 382 Length adjustment: 30 Effective length of query: 355 Effective length of database: 352 Effective search space: 124960 Effective search space used: 124960 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