Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate N515DRAFT_0006 N515DRAFT_0006 aspartate aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Dyella79:N515DRAFT_0006 Length = 399 Score = 268 bits (684), Expect = 3e-76 Identities = 146/398 (36%), Positives = 212/398 (53%), Gaps = 1/398 (0%) Query: 13 QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72 Q A R+ S I+ I +A +K G+ +I G P+F +HV +AA +A+ Sbjct: 3 QLAQRVGRAKPSAIMVIAEKARQLKAAGRDIISFSIGVPNFLPGDHVYEAAREALKHDSG 62 Query: 73 KYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPT 132 +Y + G L A + Y +++ GAKQ+L+N A LD GDE+ Sbjct: 63 QYGSNRGAEPLLDAFLRHIEALGFSGYGRMNLSIGIGAKQVLYNLAEAMLDEGDEICFAA 122 Query: 133 PYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYS 192 PYWT+Y DI I K ++ C ++L +LEAA+ + + L N+PSNP+G Y+ Sbjct: 123 PYWTTYHDIADIVGAKANVLHCGPEQNYKLVPAQLEAALQRKPKVFLFNNPSNPTGMVYT 182 Query: 193 AADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYA 252 + L +VL+++P W++ DD+Y +V+DG + +P L+ R + V+ VSK Y Sbjct: 183 REEIAALADVLVKYPDTWIVTDDIYNSMVFDGIGYHNFVFAQPELRERLVFVDSVSKTYG 242 Query: 253 MTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRR 312 M GWR+G GP + KA+ + S + + AA+VAA GPQD + + E F +R Sbjct: 243 MPGWRVGLIAGPESVAKAVTTLNSNHITSVPEVITAAAVAAFGGPQDVPRAKCEEFAGKR 302 Query: 313 DLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAV 372 D+V L AI G+ C P+GAFY F + GK + G +I D +FCA LLE VA Sbjct: 303 DVVFEALTAIPGVVCPRPQGAFYAFPDISVAFGK-SHQGTKISNDVEFCAALLEATGVAC 361 Query: 373 VPGSAFGLSPFFRISYATSEAELKEALERIAAACDRLS 410 VPGSAFG RISY A+LK LERI A +LS Sbjct: 362 VPGSAFGEPRAMRISYTCPTAQLKPGLERIQAFFAQLS 399 Lambda K H 0.318 0.134 0.393 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: 413 Number of extensions: 30 Number of successful extensions: 2 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: 410 Length of database: 399 Length adjustment: 31 Effective length of query: 379 Effective length of database: 368 Effective search space: 139472 Effective search space used: 139472 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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