Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate GFF1235 Psest_1268 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__psRCH2:GFF1235 Length = 382 Score = 192 bits (489), Expect = 1e-53 Identities = 131/359 (36%), Positives = 189/359 (52%), Gaps = 18/359 (5%) Query: 36 LTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSV-TPEET 94 L+ G PDFD PE ++EA + G +YAP G+P LRE +A K G V E Sbjct: 29 LSQGFPDFDGPEALREAVAGHVMAGHNQYAPMTGLPALREQVAAKVAGLYGRDVDAAAEV 88 Query: 95 IVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVE-TLPEEGFVPD 153 +T G QA+F QA++ PGDEVIV P + SY V+ AGGV + + +LP+ F D Sbjct: 89 TITPGATQAIFCAIQAVIRPGDEVIVFDPCYDSYEPSVQLAGGVCIHQQLSLPD--FRID 146 Query: 154 PERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYEG 213 +R+ AITPRT+ +V+N+P+NP+GA+ + L+ LA L E D YL+SDE+YEHL+++G Sbjct: 147 WQRLADAITPRTRMIVLNTPHNPSGALIDADDLDRLAALIRERDIYLLSDEVYEHLVFDG 206 Query: 214 -EHFSPGR--VAPEHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPDTI 270 EH S R + ++ K + +TGW+ GY P + + V + + T Sbjct: 207 REHASVLRHDELYQRAFVISSFGKTYHVTGWKTGYVVAPPMLSVELRKVHQYVSFTGVTP 266 Query: 271 AQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSPI 330 QWA + + A + Y+ +RDL + L R +G ++ L D S I Sbjct: 267 LQWALADFMA---AHPEHLAELPAFYQAKRDLFCDLLAGSRFSFTRAAGTYFQLADYSAI 323 Query: 331 AP--DEVRAAERLL-EAGVAVVPGTDF-----AAFGHVRLSYATSEENLRKALERFARV 381 P D+V AE L E GVA +P + F A VR +A EE LR+A ER + Sbjct: 324 RPDLDDVAMAEWLTREHGVACIPISVFYQHPPANLRLVRFCFAKREETLRQAAERLCAI 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: 358 Number of extensions: 19 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