Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate PP_0858 PP_0858 putative methionine/glutamine aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Putida:PP_0858 Length = 382 Score = 177 bits (448), Expect = 6e-49 Identities = 119/358 (33%), Positives = 181/358 (50%), Gaps = 16/358 (4%) Query: 36 LTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSV-TPEET 94 L+ G PDF+ P+ + +A R +A G +Y+P G+P LR+ +A K R G V +E Sbjct: 29 LSQGFPDFNGPQALLDAVGRHVAAGHNQYSPMTGLPALRQQVAAKVERLYGARVDADQEV 88 Query: 95 IVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFVPDP 154 +T G +A+F QA++ GDEVIV P + SY V AGG V V+ L + F D Sbjct: 89 TITPGATEAIFCAIQAVVHAGDEVIVFDPCYDSYEPSVELAGGRCVHVQ-LSDGDFRIDW 147 Query: 155 ERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYEGE 214 ++ A++PRT+ +++NSP+NP+GA+ +E L+ LA L + D YLVSDE+YEHL+Y+G Sbjct: 148 QKFSDALSPRTRMVILNSPHNPSGALITREDLDQLAALIADRDIYLVSDEVYEHLVYDGV 207 Query: 215 HFSPGRVAPE---HTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPDTIA 271 + + V+ K + +TGW+ GY P + + V T Sbjct: 208 RHASVLAHEQLYSRAFVVSSFGKTYHVTGWKTGYVIAPPALSAELRKVHQYVNFCGVTPL 267 Query: 272 QWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSPIA 331 Q A + + ++ Y+ +RDL L R +G ++ L+D S I Sbjct: 268 QCALADFMAGHP---EHIDELPAFYQAKRDLFCGLLDGSRFNFTRTTGTYFQLVDYSQIR 324 Query: 332 PD--EVRAAERLL-EAGVAVVPGTDF-----AAFGHVRLSYATSEENLRKALERFARV 381 PD +V + L E GVA +P + F VRL +A EE LR+A ER + Sbjct: 325 PDLNDVDMSLWLTREHGVATIPVSVFYQQPIPEQRLVRLCFAKREETLRQAAERLCAI 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: 328 Number of extensions: 20 Number of successful extensions: 5 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 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