Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_013135213.1 ARNIT_RS07040 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000092245.1:WP_013135213.1 Length = 426 Score = 130 bits (327), Expect = 7e-35 Identities = 96/298 (32%), Positives = 147/298 (49%), Gaps = 22/298 (7%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P ++ G A + D DG +Y+DF+ G L GHC+ + EA+ T + +F A Sbjct: 34 PPFIARGEGAYLIDIDGNKYLDFIQSWGPLIFGHCDKDIEEAVIR--TVMDGLSFGA--- 88 Query: 75 GPYLALMEQLSQFVPVSYPLAGM-LTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRT 133 P + E + V + L + +SG EA +A+++ARG TGK I+ F+G +HG + Sbjct: 89 -PSVLETELAREIVEMYDNLDKVRFVSSGTEATMSAIRLARGVTGKNDILKFEGCYHGHS 147 Query: 134 LATLNLNGK-VAPYKQRVGELPGPVYHLPYPSADTGVTCE-QALKAMDRLFSVELAVEDV 191 + L G +A + PG +P + CE ++ + + F D+ Sbjct: 148 DSLLVQAGSGMATFG--TPSSPG----VPADLTKHTLLCEYNNIENLKKCFEQS---SDI 198 Query: 192 AAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIE 251 A I EP+ G GF+ D F +A R CDE L+I DE+ +GF RT + + + Sbjct: 199 ACIIIEPIAGNMGFIPADIEFLKACREICDENNTLLIYDEVMTGF-RTSLKGTSGIVEPQ 257 Query: 252 PDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGL---GGTYSGNPISCAAALASLAQM 306 D++ K I GMP+GA KE+MA L G GT SGNP++ AA L SL ++ Sbjct: 258 ADIITFGKVIGAGMPVGAFASNKEIMAHLSPDGAVYQAGTLSGNPVAMAAGLTSLRKL 315 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: 433 Number of extensions: 20 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 416 Length of database: 426 Length adjustment: 32 Effective length of query: 384 Effective length of database: 394 Effective search space: 151296 Effective search space used: 151296 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