Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_012116197.1 XAUT_RS21405 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000017645.1:WP_012116197.1 Length = 428 Score = 359 bits (922), Expect = e-104 Identities = 190/411 (46%), Positives = 254/411 (61%), Gaps = 2/411 (0%) Query: 4 ESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR 63 ++I + IA +P+ +EVWD DG RYIDF GGI VLN GH +P V+ A++AQ Sbjct: 13 KAIPRGIATAYPVFAQKAEGSEVWDADGTRYIDFAGGIAVLNTGHRHPRVLAAVRAQLDA 72 Query: 64 LTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAII 123 TH AF P+ PY+AL E+L+ P + +L ++GAEA ENA+K+A+ ATG+ +I Sbjct: 73 YTHTAFQIVPYEPYVALCERLNAIAPFTGAAKSILFSTGAEAVENAVKIAKAATGRTGVI 132 Query: 124 AFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFS 183 +F GGFHGRT T+ L GKV PYK++ G P ++HLP+P AD GV+ LKA+D LF Sbjct: 133 SFSGGFHGRTALTMALTGKVLPYKKKFGISPPGIFHLPFPCADHGVSVADTLKALDYLFR 192 Query: 184 VELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243 ++ +DVAA I EPVQGEGGFL ALR+ CD GI++I DE+Q+GF RTG+ F Sbjct: 193 ADIGPQDVAAIIIEPVQGEGGFLPAPTELLVALRQTCDAHGIVLIADEVQTGFARTGRMF 252 Query: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303 G+EPDL+ +AKS+AGG PL V+GR+ +M A GGLGGTY+GNPI+CAAALA L Sbjct: 253 GIEHSGVEPDLVTVAKSLAGGFPLSGVIGREAIMDAAEPGGLGGTYAGNPIACAAALAVL 312 Query: 304 AQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ 363 + +E L I R + IG + G GAM + G+ P Sbjct: 313 DVIAEEKLVERANAIGARIKDALTRMALRNDAVAIGSIRGPGAMVAFDVVKKRGTVEPDA 372 Query: 364 LA--KVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 A +V +AA A GL+L+ G + IRLL PLTI +L+EGL LE+ L Sbjct: 373 DAARRVTQAALADGLILITCGVYGNTIRLLNPLTIPDALLDEGLGKLERAL 423 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: 522 Number of extensions: 18 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: 428 Length adjustment: 32 Effective length of query: 384 Effective length of database: 396 Effective search space: 152064 Effective search space used: 152064 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 Jul 25 2024. The underlying query database was built on Jul 25 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