Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate Dsui_3376 Dsui_3376 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__PS:Dsui_3376 Length = 388 Score = 170 bits (431), Expect = 5e-47 Identities = 118/358 (32%), Positives = 172/358 (48%), Gaps = 20/358 (5%) Query: 34 VALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSVTPEE 93 + L+ G PDF + +A +A+ G+ +YAP G+PELR+A+A K + G + E Sbjct: 33 INLSQGFPDFQADRSLFDAVHQAMLDGRNQYAPMTGLPELRQAIAAKVQALYGTAYDAES 92 Query: 94 TI-VTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFVP 152 I VT G QALF A PGDEVIV +P + SY + G V L + P Sbjct: 93 EITVTAGATQALFTAIAAFAGPGDEVIVFAPVYDSYVPAIETVGAKAVYAN-LRYPDYKP 151 Query: 153 DPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYE 212 D VR ITPRT+ ++VN+P+NPTG++ LEALA L + + ++ DE+YEH+ +E Sbjct: 152 DWNEVRALITPRTRMIIVNTPHNPTGSLLDAADLEALAELTRDTNIVVLGDEVYEHICFE 211 Query: 213 GEHFSPGRVAPE---HTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPDT 269 GEH S R PE +L V+ K + +TGW+IGY G ++ V + + Sbjct: 212 GEHQSLAR-HPELAARSLIVSSFGKTYHITGWKIGYCYGAAALMAEFRKVHQFNVFTVHA 270 Query: 270 IAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVL--MDT 327 +Q + + E YR++RD + L + + G ++ L D Sbjct: 271 PSQVGLAAFMADHSRHLQLAEF----YRQKRDFFRQQLAGTKFELLPSRGTYFQLARYDA 326 Query: 328 SP----IAPDEVRAAERLLEAGVAVVPGTDFAAFGH----VRLSYATSEENLRKALER 377 P PD A E GVAV+P + F G VR +A E L A E+ Sbjct: 327 LPGPAADLPDTEFAQWLTREVGVAVIPVSVFYPDGRDDKVVRFCFAKQESTLAAAGEK 384 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: 352 Number of extensions: 23 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: 388 Length adjustment: 30 Effective length of query: 355 Effective length of database: 358 Effective search space: 127090 Effective search space used: 127090 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