Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_900105005.1:WP_090273343.1 Length = 404 Score = 192 bits (488), Expect = 2e-53 Identities = 139/402 (34%), Positives = 196/402 (48%), Gaps = 36/402 (8%) Query: 21 GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80 G + +WD G+ YID GGI V +LGH +P +VEA+ QA +L H + N + P L L Sbjct: 30 GDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQKLWHVS-NIMTNEPALRL 88 Query: 81 MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGRTL 134 ++L V ++ + NSGAEA E A K+AR K IIA FHGRTL Sbjct: 89 ADKL---VAATFADKVLFVNSGAEANEAAFKLARRWAHDQSGPDKHEIIACSNSFHGRTL 145 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAF 194 T+++ G+ Y Q G + H+PY + A++ S E A Sbjct: 146 FTVSVGGQ-PKYSQGFGPAISGISHVPYND----------IAALEAQIS-----ERTCAV 189 Query: 195 IFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDL 254 + EPVQGEGG + + +A+R CD+ L+I DE+QSG GRTG+ +A+ G+ PD+ Sbjct: 190 VVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRTGKLYAYMHSGVAPDI 249 Query: 255 LLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM-TDENLAT 313 L AK I GG P+ A++ + AL G G TY GNP+ CA A L + T + L Sbjct: 250 LTSAKGIGGGFPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVLDIINTPQVLDG 309 Query: 314 WGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARA 373 GERQ Q R A L + + G G + G A Q +VM A+ Sbjct: 310 VGERQAQLTAGL--RILADELGVF-SEIRGQGLLIGAVLAER----WRGQAGQVMRLAQE 362 Query: 374 RGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 GLL++ +G ++RL L I + E L + L L Sbjct: 363 EGLLVLQAG--ADVVRLAPSLIIPEADIREALGRMRAALLRL 402 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: 423 Number of extensions: 20 Number of successful extensions: 4 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: 404 Length adjustment: 31 Effective length of query: 385 Effective length of database: 373 Effective search space: 143605 Effective search space used: 143605 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