Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate PfGW456L13_2943 Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2943 Length = 395 Score = 208 bits (529), Expect = 3e-58 Identities = 125/378 (33%), Positives = 206/378 (54%), Gaps = 17/378 (4%) Query: 28 KIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAI 87 +I RA A++ +G V++L G+PDFDTP+ + QAA ++ G+T Y A+ G+ L+ +I Sbjct: 19 QIHDRALALREQGVDVLLLSIGDPDFDTPQPIVQAAIGSLLAGDTHYPAVRGSQGLRDSI 78 Query: 88 REKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEG 147 +R +G A + + V GA+ +++ LDPGDEV++ P + +Y + C Sbjct: 79 ARHHRRRSGQAVDAQHVIVFPGAQCAVYSVAQCLLDPGDEVLVAEPMYVTYEGVFGACGA 138 Query: 148 KPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHP 207 K V + + +GFR+ + A ITP TR +LLNSP+NPSGA+ ++ L + +RH Sbjct: 139 KVVPVPVRSQNGFRVDPADVAALITPNTRAMLLNSPNNPSGASLPLTAWKALAALCIRH- 197 Query: 208 HVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPREL 267 +WL+ D++Y ++++G ++PA L PG+ RT T+N +SK++AM+GWR+G+ GP+ L Sbjct: 198 DLWLISDEVYSELLFEG-EHISPASL-PGMAERTATINSLSKSHAMSGWRVGWVIGPQSL 255 Query: 268 IKAMAVVQ-SQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLD 326 + + + P I AA + AL+ + + E +++RRDLV LN G+ Sbjct: 256 CEHLVNLSLCMLFGIPDFIQNAAQL-ALDENLPHVAQMREEYRQRRDLVCASLNLCPGIQ 314 Query: 327 CRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGLSP--FF 384 P+G + V+ V +G + F LL+ V+V+ G AFG S Sbjct: 315 AIRPDGGMF-------VMVDVRQTGLSAQ---HFAERLLDGYGVSVLAGEAFGPSAAGHI 364 Query: 385 RISYATSEAELKEALERI 402 RI +L +A RI Sbjct: 365 RIGLVVDRPKLADACRRI 382 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: 432 Number of extensions: 19 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: 410 Length of database: 395 Length adjustment: 31 Effective length of query: 379 Effective length of database: 364 Effective search space: 137956 Effective search space used: 137956 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 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