Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_012991510.1 THAL_RS02335 glutamate-1-semialdehyde-2,1-aminomutase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000025605.1:WP_012991510.1 Length = 424 Score = 136 bits (343), Expect = 1e-36 Identities = 97/307 (31%), Positives = 147/307 (47%), Gaps = 39/307 (12%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 PI + + +WD +GK YIDF+ G L LGH +P VV ++ Q +R Y Sbjct: 32 PIVVREAKGCRLWDVEGKEYIDFLMSWGPLILGHAHPYVVSEVERQLSRGMSYGLTCYEE 91 Query: 75 GPYLALMEQLSQFVPVSYPLAGML--TNSGAEAAENALKVARGATGKRAIIAFDGGFHGR 132 +L++ V S P M+ +SG EA +A+++ARG TG++ ++ F+G +HG Sbjct: 92 -------IRLAELVVSSVPSVEMVRFVSSGTEATMSAIRLARGYTGRKFVVKFEGCYHGH 144 Query: 133 ----------TLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLF 182 +ATL + G + E+ G LPY D L Sbjct: 145 YDGLLVSAGSGVATLGIPGTPGVPE----EIAGLTLVLPYNDTDA------------VLS 188 Query: 183 SVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQR 242 + E ED+A I EPV G G + F + LR + G ++I DE+ + F R Sbjct: 189 TFERYGEDIACVIVEPVAGNMGVVLPSEGFLEVLREVTRKYGAVLIFDEVITNF-RLSVG 247 Query: 243 FAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMA-ALPKGGL--GGTYSGNPISCAAA 299 A I+PD+ + K + GGMPLGA G+KE+M+ P+G + GT SGNP+S Sbjct: 248 GAQEYYAIDPDITCMGKILGGGMPLGAYGGKKEIMSHVAPEGKVYQAGTLSGNPVSVVCG 307 Query: 300 LASLAQM 306 A+L ++ Sbjct: 308 RATLEEL 314 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: 437 Number of extensions: 20 Number of successful extensions: 5 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: 424 Length adjustment: 32 Effective length of query: 384 Effective length of database: 392 Effective search space: 150528 Effective search space used: 150528 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