Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_003173355.1:WP_109969613.1 Length = 384 Score = 207 bits (528), Expect = 3e-58 Identities = 145/407 (35%), Positives = 207/407 (50%), Gaps = 47/407 (11%) Query: 11 AIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-F 69 A I ++ G V D DGK+Y+D V GI V + GHC+P VV+AI QA L H + Sbjct: 18 AFSREIMITKGSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIHCSNL 77 Query: 70 NAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGF 129 PH AL ++L + + +NSGAEA E ALK+AR TG++ IA +GGF Sbjct: 78 FYVPHQG--ALAKKLVEISGLPGNAKAFFSNSGAEAMEGALKLARIRTGRKEFIACEGGF 135 Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189 HGRT+ +L K A + + P + +PY QALK E Sbjct: 136 HGRTMGSLACTHKPAIREPFMPLQPFTSF-VPYGDV-------QALKGA--------ITE 179 Query: 190 DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLG 249 + AA I EP+QGEGG + P + + +R CD +G+L+I+DE+QSG GRTG FAF G Sbjct: 180 ETAAVILEPIQGEGGVIIPPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFAFQEEG 239 Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD- 308 I PD++ +AK++A G P+GA+V R+ L K G T++G PI+CAAALAS+ + Sbjct: 240 IHPDIITMAKAMASGFPMGAIVAREGL--EFGKSEHGSTFAGGPIACAAALASIDVIGKV 297 Query: 309 -ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKV 367 +A GER A+ R K G M GI + A V Sbjct: 298 LPEVAAKGERFRAALAHLNPRVK--------------GLMIGITIGD--------HCADV 335 Query: 368 MEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 + GLL+ + A +RL+ PLTI +++ I+ +++ Sbjct: 336 QKECAVHGLLV--NCAAHGNLRLVPPLTITNAEIDKATGIINAAVSK 380 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: 456 Number of extensions: 29 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: 384 Length adjustment: 31 Effective length of query: 385 Effective length of database: 353 Effective search space: 135905 Effective search space used: 135905 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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