Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate WP_011423889.1 RHE_RS02610 acetylornithine transaminase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000092045.1:WP_011423889.1 Length = 399 Score = 194 bits (492), Expect = 5e-54 Identities = 140/405 (34%), Positives = 200/405 (49%), Gaps = 43/405 (10%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-FNAAP 73 P+ G + G+RY+DF G+ V ++GH NP VV A++ QA ++ H + P Sbjct: 15 PLRFERGEGVWLITESGERYLDFGAGVAVTSVGHGNPHVVAALKEQADKVWHLSNIYEIP 74 Query: 74 HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDG 127 LA + ++ TNSGAEA E A+K AR G + II F+G Sbjct: 75 GQERLA-----KRLTDATFADKVFFTNSGAEALECAIKTARRYQFSKGHPERFHIITFEG 129 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 FHGRTLAT+ G+ Y + G +P+ + +V A Sbjct: 130 AFHGRTLATIAAGGQ-EKYLEGFGPKAPGFDQVPFGDIE----------------AVRAA 172 Query: 188 VEDV-AAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 + D AA + EPVQGEGG F +ALRR CDE G+L+I+DE+Q+G GRTG+ FA Sbjct: 173 ITDATAAILIEPVQGEGGVRPATTEFMKALRRICDENGLLLILDEVQTGVGRTGKLFAHE 232 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306 GI PD++ +AK I GG PLGA + E + + G G TY GNP++ A A L + Sbjct: 233 WSGITPDIMAVAKGIGGGFPLGACLATAEAASGMKAGTHGSTYGGNPLAMAVGSAVLDVI 292 Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSP-YIGRLTGVGAMRGIEFANADGSPAPAQLA 365 E ++ A+V R P I + G G + G++ A A Sbjct: 293 LAEGFLE--HVRDVALVFRQGLASLKDRYPDVIEDIRGEGLLLGVK--------AAVPSA 342 Query: 366 KVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQ 410 ++++A RA LL +P+G ++IRLL PL + AE EGL LE+ Sbjct: 343 ELLQAIRAAHLLGVPAGD--NVIRLLPPLVVTAEEAREGLARLER 385 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: 440 Number of extensions: 27 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: 399 Length adjustment: 31 Effective length of query: 385 Effective length of database: 368 Effective search space: 141680 Effective search space used: 141680 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