Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 344 bits (882), Expect = 3e-99 Identities = 177/389 (45%), Positives = 249/389 (64%), Gaps = 7/389 (1%) Query: 4 LSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTK 63 +SD L R+KPS T+AV KA EL A G V+ L GEPDF TP++++ AAK AID G T+ Sbjct: 3 ISDRLTRIKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAIDQGFTR 62 Query: 64 YTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAP 123 YT V GIPEL++A+C F R G++ V GGKQ LYN LNPGDEV++PAP Sbjct: 63 YTQVPGIPELRQAVCGYFARFYGVEAPMEATVVTNGGKQALYNLFQCLLNPGDEVLVPAP 122 Query: 124 YWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTR 183 YWVSYP +V LAGG PV VA+ E GFK+TPE+L+ A+TP+T+ + NSPSNPTGA Y+R Sbjct: 123 YWVSYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSR 182 Query: 184 AELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCM 243 AE A+ E + ++++SD++Y+ LV++ + + + NG++K + M Sbjct: 183 AETDAIMEWAIAR-DLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTFAM 241 Query: 244 TGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRD 303 TGWR+GYA +LI+AM IQ QSTSN CS+AQ AAL AL+GP + + +++F+RRRD Sbjct: 242 TGWRVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRRRD 301 Query: 304 LVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVV 363 L +++ GV CP P+GAFY++ D+ + D + + ++E+ VA+V Sbjct: 302 LAHGIVSSWPGVICPKPDGAFYLFADMRALFTPA------LPDSASLCTYIMEQANVALV 355 Query: 364 FGAAFGLSPNFRISYATADEVLREACARI 392 GAAFG R SYA +D+ L A ++ Sbjct: 356 PGAAFGDDACLRFSYAVSDDTLMIALDKV 384 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: 475 Number of extensions: 25 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: 400 Length of database: 390 Length adjustment: 31 Effective length of query: 369 Effective length of database: 359 Effective search space: 132471 Effective search space used: 132471 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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