Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate 352902 BT3375 aspartate aminotransferase (NCBI ptt file)
Query= curated2:O67781 (394 letters) >FitnessBrowser__Btheta:352902 Length = 386 Score = 253 bits (645), Expect = 9e-72 Identities = 134/390 (34%), Positives = 232/390 (59%), Gaps = 9/390 (2%) Query: 8 RVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKTKYAP 67 ++S + S + ++T + L K +VI F G+PD D IKEA +A+ EG+T+Y+P Sbjct: 3 QLSEITNSISPSLTRRLFNLAQKYDNVIDFTLGDPDIHPHDKIKEAGCKAILEGRTRYSP 62 Query: 68 SAGIPELREAIAEKLLKENKVEYKPS-EIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYW 126 +AG+ ELRE I+ + + +EY P+ EI+V+ G L+L +AIL+ GDEV++P+PYW Sbjct: 63 NAGLLELREIISSRYKLQYNIEYNPTNEIMVTVGGMEGLYLTLLAILNRGDEVIIPAPYW 122 Query: 127 VTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEE 186 + Y + + G P+ +S+E++++ +T +TKAI++N+P+NP+G + ++ Sbjct: 123 INYVQMVCMCSGEPIITAPVSTNDLSISIENIRKAITPKTKAIILNTPSNPSGRIISDDS 182 Query: 187 LKKIAEFCVERGIFIISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMTGW 246 +++IA+ +E + +I+DE Y+ +Y +A F S + D++K T +N+ SK + MTGW Sbjct: 183 IQQIAQIAIENDLIVITDEVYKTLLYDNAHFKSIVT-CDKMKERTVVINSLSKEFCMTGW 241 Query: 247 RIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRRDT 306 R+GY+A P E V+ + +QY A+EAL+N S+ + M F RR+ Sbjct: 242 RLGYIAAPSELISVMTMFQENIAACAPLPSQYAAIEALRN--SEKYSAGMIEEFTLRRNV 299 Query: 307 AVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAFG-- 364 +EE++KI + V P+G FY + + K + + LLEK +VAVVPG +G Sbjct: 300 LLEEVAKIKTITVDAPQGTFYAMLNIKSTGLK---SEEFAYALLEKEQVAVVPGITYGDC 356 Query: 365 APGFLRLSYALSEERLVEGIRRIKKALEEI 394 F+R+++ L ++ EGI+R+K+ +E + Sbjct: 357 CEDFIRIAFTLDIYKIKEGIQRLKRFVESL 386 Lambda K H 0.317 0.135 0.383 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: 376 Number of extensions: 17 Number of successful extensions: 6 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: 394 Length of database: 386 Length adjustment: 31 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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 (21.6 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