Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate Pf6N2E2_5269 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5269 Length = 416 Score = 659 bits (1701), Expect = 0.0 Identities = 319/415 (76%), Positives = 368/415 (88%) Query: 1 MNQESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQ 60 M+ E+ISQSI+IVHP++LSHG+NAEVWD DGKRYIDFVGGIGVLNLGHC+P +VEAI+ Q Sbjct: 1 MSSETISQSISIVHPVSLSHGKNAEVWDADGKRYIDFVGGIGVLNLGHCHPRIVEAIREQ 60 Query: 61 ATRLTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKR 120 ATRLTHYAFNAAPH PY+ LME+L+ FVPV YP++GMLTNSGAEAAENALK+ RGATG+ Sbjct: 61 ATRLTHYAFNAAPHTPYIELMERLAAFVPVDYPVSGMLTNSGAEAAENALKIVRGATGRT 120 Query: 121 AIIAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDR 180 A+IAFDG FHGRTLATLNLNGKVAPYKQ+VG LPGPVYHLPYPS D GVT E+AL+AM+R Sbjct: 121 AVIAFDGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVYHLPYPSKDNGVTREEALRAMER 180 Query: 181 LFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTG 240 LFSVE+ V DVA FI EPVQGE GFLA+D FAQALR+FCD++GI++I+DEIQSGFGRTG Sbjct: 181 LFSVEIDVNDVACFIVEPVQGEAGFLAMDVLFAQALRQFCDDKGIVLIVDEIQSGFGRTG 240 Query: 241 QRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAAL 300 QRFAF RLGIEPDL+LL KSIAGG+PLGAVVGRK L+ LPKGGLGGTYSGNPI+CAAAL Sbjct: 241 QRFAFSRLGIEPDLVLLGKSIAGGVPLGAVVGRKALLDNLPKGGLGGTYSGNPIACAAAL 300 Query: 301 ASLAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPA 360 A+L +MTD NL WG +QE+AIVSRY+ W+ GL+PY+GRLTGVGAMRGIE +ADG+PA Sbjct: 301 ATLDEMTDANLHAWGSQQEEAIVSRYQSWRNRGLTPYLGRLTGVGAMRGIELTHADGTPA 360 Query: 361 PAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 AQL +++ AR GLLLMPSGK+RHI+RLLAPLT E VLEEGLDILE CLA+L Sbjct: 361 SAQLTQLLALARESGLLLMPSGKSRHIVRLLAPLTTEPNVLEEGLDILEACLAKL 415 Lambda K H 0.320 0.137 0.402 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: 675 Number of extensions: 17 Number of successful extensions: 1 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: 416 Length of database: 416 Length adjustment: 31 Effective length of query: 385 Effective length of database: 385 Effective search space: 148225 Effective search space used: 148225 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 (21.8 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