Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate GFF4517 PS417_23120 aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__WCS417:GFF4517 Length = 382 Score = 160 bits (406), Expect = 4e-44 Identities = 113/371 (30%), Positives = 177/371 (47%), Gaps = 18/371 (4%) Query: 28 AAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYTAVDGIPELKRAICEKFERENGL 87 AA + L G PDF P + A + I G +Y + G+P L++ + K R G Sbjct: 21 AAETGALNLSQGFPDFSGPQGLLDAVGKHIALGHNQYAPMTGLPVLRQQVAAKIARSYGA 80 Query: 88 KY-TPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSYPDMVLLAGGTPVSVAAGM 146 ++VT+ G + ++ A+ A + GDEVI+ P + SY V LAGG V V + Sbjct: 81 TVDADSEVTITPGATEAIFCAIQAVIRNGDEVIVFDPSYDSYEPSVELAGGRCVHVQLSL 140 Query: 147 ETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAALCEVLMRHPQVWIMSDDM 206 +GF L E+++AA++PRT+ I N+P NPTGA +RAEL L E L+R ++++SD++ Sbjct: 141 -SGFALDFEKIKAALSPRTRMIILNTPHNPTGALISRAELDQLAE-LIRDRDIYLVSDEV 198 Query: 207 YEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRIGYAAGPVELIRAMGTIQS 266 YEHLVFD + E LY R + K Y +TGW+ GY P L + + Sbjct: 199 YEHLVFDGVAHVSVLAHEE-LYPRAFVVSSFGKTYHVTGWKTGYVVAPPALTAELRKVHQ 257 Query: 267 QSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVVSMLNEAKGVTCPNPEGAFYV 326 + QYA + ++ E + +Q +RDL +L A + G ++ Sbjct: 258 YVNFCGVTPLQYALADFMAEHPEHVEELPAFYQAKRDLFCDLL-AASRFSFTRVTGTYFQ 316 Query: 327 YPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGAAFGLSPN-----FRISYATA 381 D S DD A + + E GVA + + F +P R+ +A Sbjct: 317 LVDYSQI--------RPDLDDVAMSLWMTREHGVATIPVSVFYQTPPQGQRLVRLCFAKR 368 Query: 382 DEVLREACARI 392 +E LR+A ++ Sbjct: 369 EETLRQAAEKL 379 Lambda K H 0.318 0.134 0.399 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: 398 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: 400 Length of database: 382 Length adjustment: 31 Effective length of query: 369 Effective length of database: 351 Effective search space: 129519 Effective search space used: 129519 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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