Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate RR42_RS12545 RR42_RS12545 aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS12545 Length = 410 Score = 155 bits (393), Expect = 2e-42 Identities = 115/389 (29%), Positives = 188/389 (48%), Gaps = 23/389 (5%) Query: 19 VTNKARELAAAGRDVIGLGAGEP---DFDTPDNIKAAAKRAIDAGRTKYTAVDGIPELKR 75 V KA+++ G +I L G FD P+ I+ R + Y+ GI ++ Sbjct: 21 VLEKAKQMEEEGHKIIKLNIGNLAVFGFDAPEEIQQDMMRNLP-NSAGYSDSKGIFAARK 79 Query: 76 AICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSYPDMVLLA 135 AI +++N + VG G +++ ++ A LN GDEV++PAP + + V L+ Sbjct: 80 AIMHYTQQKNIEGVGLDDIYVGNGASELIVMSMNALLNSGDEVLVPAPDYPLWTAAVSLS 139 Query: 136 GGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAALCEVLMR 195 GGTPV + + + A ITP TK + +P+NPTGA Y+ A L ++ + Sbjct: 140 GGTPVHYVCDEANEWMPDLDDIRAKITPNTKAIVVINPNNPTGALYSDALLKSIVAIARE 199 Query: 196 HPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRIGYAAGPV 255 H + I +D++Y+ +++D T+ A + + T+T NG+SK Y G+R G+ Sbjct: 200 HGLI-IFADEIYDKVLYDGHSHTSIAALSTDVL--TVTFNGLSKNYRSCGYRAGWMVVSG 256 Query: 256 ELIRAMGTIQSQSTSNPCSI-----AQYAALEALSGPQEF--LATNREAFQRRRDLVVSM 308 + A+ I+ + + + AQ+A AL G Q L +R+RDL + Sbjct: 257 DKRPALDYIEGLNMLSSMRLCANVPAQWAIQTALGGYQSINDLVGEGGRLRRQRDLAHEL 316 Query: 309 LNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVVFGAAF 368 + + GVTC P+ A Y++P K I DD+ F LL+E+ V +V G F Sbjct: 317 ITQIPGVTCVKPKAALYLFP-------KLDLSMYPIQDDQEFIYELLQESKVLLVQGTGF 369 Query: 369 --GLSPNFRISYATADEVLREACARIQAF 395 G +FRI + +E LREA +R+ F Sbjct: 370 NWGKPDHFRIVFLPHEEDLREAISRVGRF 398 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: 416 Number of extensions: 17 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: 410 Length adjustment: 31 Effective length of query: 369 Effective length of database: 379 Effective search space: 139851 Effective search space used: 139851 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