Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_009547763.1 CCE_RS14630 aspartate aminotransferase family protein
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000017845.1:WP_009547763.1 Length = 422 Score = 192 bits (488), Expect = 2e-53 Identities = 133/408 (32%), Positives = 210/408 (51%), Gaps = 35/408 (8%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 PI + G +WDT GK Y+DFV GI LGH +PA+V+ + Q L H + + Sbjct: 31 PIAIDRGEGCRLWDTKGKEYLDFVAGIATCTLGHGHPALVKTVSEQIQSLHHVS-----N 85 Query: 75 GPYLALMEQLSQFVPVSYPLAGML--TNSGAEAAENALKVARGATG-------KRAIIAF 125 Y+ +L+Q++ + + A + NSGAEA E A+K+ R + + I+ Sbjct: 86 LYYIPQQGELAQWM-IEHSCADKVFFCNSGAEANEAAIKLIRKYSHTVLDFLEQPVILTA 144 Query: 126 DGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFS-V 184 FHGRTLAT+ G+ + +PG Y +PY +KA++ + + Sbjct: 145 KASFHGRTLATITATGQPKYQQDFEPLMPGFAY-VPYND----------IKAIEHAIADI 193 Query: 185 ELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244 + VAA + EP+QGEGG + + LR+ CDE IL++ DE+Q G GR+G+ + Sbjct: 194 DEGNRRVAAIMLEPLQGEGGVRPGEIEYFLRLRKICDENNILLVFDEVQVGVGRSGKLWG 253 Query: 245 FPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLA 304 + LG+EPD+L AK +AGG+P+GA++ KE L G T+ GNP++CAAAL L Sbjct: 254 YENLGVEPDVLTSAKGLAGGIPIGAMM-CKEFCNVLTPGTHASTFGGNPLACAAALTVLK 312 Query: 305 QMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQL 364 + +EN+ + + + + +R R A + G G + G+E N + S + Sbjct: 313 TIEEENILQNVQARGEQLRTRL-RAIAQKDPTLFTDVRGWGLINGLEI-NEEMSITSIDI 370 Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 K AA GLLL P+G ++R + PL + E + + D+LE + Sbjct: 371 VK---AAMEEGLLLAPAGP--KVLRFVPPLIVTEEEINQAADLLETAI 413 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: 423 Number of extensions: 19 Number of successful extensions: 6 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: 422 Length adjustment: 32 Effective length of query: 384 Effective length of database: 390 Effective search space: 149760 Effective search space used: 149760 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 10 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