Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate Pf1N1B4_849 Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_849 Length = 382 Score = 165 bits (418), Expect = 2e-45 Identities = 119/386 (30%), Positives = 188/386 (48%), Gaps = 19/386 (4%) Query: 13 PSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYTAVDGIPE 72 P+ I + + +LAA I L G PDFD P ++ A R I +G +Y+ + G+P Sbjct: 7 PNVGITIFTQMSQLAAQ-TGAINLSQGFPDFDGPQALRDAVGRHIASGHNQYSPMTGLPV 65 Query: 73 LKRAICEKFERENGLKY-TPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSYPDM 131 L++ I K R G ++VTV G Q ++ A+ A ++ GDEVI+ P + SY Sbjct: 66 LRQQIAAKIARSYGAHVDADSEVTVTPGATQAIFCAIQAVIHSGDEVIVFDPAYDSYEPS 125 Query: 132 VLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAALCE 191 V LAGG V V G+ F + ++L A++PRT+ I NSP NP+GA +RAEL L Sbjct: 126 VELAGGRCVHVQLGL-NDFSIDFQKLADALSPRTRMIILNSPHNPSGALISRAELDQLA- 183 Query: 192 VLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRIGYA 251 L+R ++++SD++YEHLVFD + E LY R + K Y +TGW+ GY Sbjct: 184 ALIRDRDIYVISDEVYEHLVFDGVSHVSVLAHEE-LYQRAFVVSSFGKTYHVTGWKTGYV 242 Query: 252 AGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVVSMLNE 311 P L + + + + QYA + ++ E + +Q +RDL +L+ Sbjct: 243 VAPPALTAELRKVHQYVSFCGVTPLQYALADYMAEHPEHVEELPGFYQAKRDLFCDLLSP 302 Query: 312 AKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGAAFGLS 371 ++ + G ++ D S +D A + E GVA + + F + Sbjct: 303 SR-FSFTRVAGTYFQLVDYSQI--------RPDLNDVEMALWMTREHGVASIPISVFYQT 353 Query: 372 PN-----FRISYATADEVLREACARI 392 P R+ +A +E LREA A++ Sbjct: 354 PPEGQRLVRLCFAKREETLREAAAKL 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: 399 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: 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