Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate 8500823 DvMF_1564 aminotransferase class I and II (RefSeq)
Query= curated2:O67781 (394 letters) >FitnessBrowser__Miya:8500823 Length = 400 Score = 232 bits (592), Expect = 1e-65 Identities = 145/393 (36%), Positives = 217/393 (55%), Gaps = 20/393 (5%) Query: 5 LASRVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKT- 63 +A RV +++ S T + L AK + G G P F TPD I EA RALR+ T Sbjct: 13 VAERVRNIRISATKLMPM----LAAKVGGCVSLGQGVPSFRTPDHIVEAVCRALRDDPTA 68 Query: 64 -KYAPSAGIPELREAIAEKLLKENKVEYKP-SEIVVSAGAKMVLFLIFMAILDEGDEVLL 121 +Y+ G+P LREAIA +L + P +EI V+ GA L +I + +++ GDEV++ Sbjct: 69 GRYSLQPGMPALREAIAADILARKGARFDPETEIGVTVGAMEALVMIMLTVVERGDEVII 128 Query: 122 PSPYWVTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAV 181 PSP + ++ EQ+ GVPV VPL+ + L +E V+ VT RT+AI++ SP NPTG V Sbjct: 129 PSPGYASHAEQVLMAEGVPVHVPLRAAD-WGLDVEAVRFAVTPRTRAIIVCSPGNPTGGV 187 Query: 182 YEEEELKKIAEFCVERGIFIISDECYEYFVYGD---AKFVSPASFSDEVKNITFTVNAFS 238 Y++ +++ + + +ER + +I D+ Y+Y VYG+ SP S E++ TVN+FS Sbjct: 188 YDDADVRALCDLALERDLVLIVDDTYDYMVYGEQPGTPRFSPVS-QPELRRHVITVNSFS 246 Query: 239 KSYSMTGWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRN 298 K Y++TGWR+GYVA + + ++ + T +Q+ AL AL P +D V+ MR Sbjct: 247 KKYALTGWRVGYVAADAAWMAELLKVHDATAVCAPTVSQHAALAALTGP--QDCVDVMRA 304 Query: 299 AFERRRDTAVEELSKI-PGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAV 357 A RRD L + P V P GAFY + Y + ++ +LE+A+V Sbjct: 305 ALTARRDLTCRRLDALAPHFAYVPPRGAFYA---MARYTFTDADSMTVARRMLEEARVIT 361 Query: 358 VPGSAFGAPG--FLRLSYALSEERLVEGIRRIK 388 VPG +FG G LRLS+ + E L E RI+ Sbjct: 362 VPGGSFGPTGERHLRLSFGMDEAELTEAFDRIQ 394 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: 375 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 394 Length of database: 400 Length adjustment: 31 Effective length of query: 363 Effective length of database: 369 Effective search space: 133947 Effective search space used: 133947 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