Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 199 bits (505), Expect = 2e-55 Identities = 149/413 (36%), Positives = 214/413 (51%), Gaps = 46/413 (11%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P+ L G VWDT G+ Y+DFV GI LGH +P +V+AI Q +L H + + Sbjct: 35 PLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHHVS-----N 89 Query: 75 GPYLALMEQLSQFVPV-SYPLAGMLTNSGAEAAENALKVAR--GATGKRA----IIAFDG 127 Y+ QL+ ++ S NSGAEA E A+K+AR G T A I+ Sbjct: 90 LYYIPEQGQLAAWLTANSCADRVFFCNSGAEANEAAIKLARKHGNTVLEAENPIILTAQA 149 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 FHGRTLA + G+ Y + L ++PY AL+A L ++ A Sbjct: 150 SFHGRTLAAVTATGQ-PKYHKGFQPLVQGFRYVPYNDL-------AALEAT--LAELDAA 199 Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247 E VAA + EP+QGEGG D A+ QA+R+ CD+R +L+I+DE+Q G GR+GQ + + Sbjct: 200 GETVAAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLWGYEN 259 Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM- 306 LGIEPD +AK + GG+P+GA++ K L G T+ GNP++C A LA +AQ+ Sbjct: 260 LGIEPDAFTVAKGLGGGVPIGALL-VKASCNILQAGEHASTFGGNPLACRAGLA-IAQVM 317 Query: 307 -TDENLATWGERQE------QAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSP 359 D+ LA R E Q +V RY A + G G + G+ N D + Sbjct: 318 ERDQLLANVQARGEQLRAGLQELVDRYPNLLAG--------VRGWGLINGLVLRN-DPNV 368 Query: 360 APAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 P L K AA +GLLL+P+G ++R + PL + A ++E L + E+ L Sbjct: 369 TPIALVK---AAIEQGLLLVPAG--AEVVRFVPPLIVSAAEIDEALAMTERAL 416 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: 432 Number of extensions: 21 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 Sep 17 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