Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= SwissProt::Q88FI7 (416 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 Length = 430 Score = 353 bits (907), Expect = e-102 Identities = 189/412 (45%), Positives = 255/412 (61%), Gaps = 4/412 (0%) Query: 6 ISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLT 65 + + + HP+ + + +E+WD DGKRY+DFVGGIGVLN+GH +P VV A+QAQ +++ Sbjct: 19 VPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKVS 78 Query: 66 HYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAF 125 H F + PYL L ++L + + SGAEA ENA+K+AR T + A+IAF Sbjct: 79 HACFQVVAYKPYLDLAQRLCEMIGGQESYKAAFFTSGAEAVENAVKIARAHTNRSAVIAF 138 Query: 126 DGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVE 185 GGFHGRTL L G PYKQ G V+H PYP+A GVT + ALKA+D L + + Sbjct: 139 RGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSDMALKALDELLATQ 198 Query: 186 LAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAF 245 +A E VAA I EPVQG+GGFL+ F QALR + GI++I+DEIQ+GFGRTG+ F F Sbjct: 199 VAPERVAAIIIEPVQGDGGFLSAPTEFLQALRALTAKHGIVLILDEIQTGFGRTGKWFGF 258 Query: 246 PRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQ 305 GI+PDL+ +AKS+AGG+PL VVG+ E+M A GGLGGTY GN +SCAAALA + Sbjct: 259 QHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEA 318 Query: 306 MTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAP-AQL 364 E L GE + + R +A P IG + G G M IE D + P A L Sbjct: 319 YEQEQLLARGEALGERLREGLLRLQAR--YPRIGDVRGSGFMLAIELIKDDDARTPDADL 376 Query: 365 -AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 ++++ ARA GLL++ G R+++R LAPL ++E L IL+ LA + Sbjct: 377 NQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQVDEALQILDAALARV 428 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: 550 Number of extensions: 19 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: 416 Length of database: 430 Length adjustment: 32 Effective length of query: 384 Effective length of database: 398 Effective search space: 152832 Effective search space used: 152832 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