Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_061535420.1 CAter10_RS16755 acetylornithine transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_001584165.1:WP_061535420.1 Length = 400 Score = 171 bits (432), Expect = 5e-47 Identities = 135/421 (32%), Positives = 208/421 (49%), Gaps = 61/421 (14%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY--AFNAA 72 P+ G + D GKRY+D++ G V LGH + +A+ AQ+ ++ + AF A Sbjct: 19 PLVFVEGDGMWMTDHTGKRYLDYLQGWAVNALGHSPQCIQDALVAQSKKIINPSPAFYNA 78 Query: 73 PHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR---------GATGKRAII 123 P L+ S F V + TNSGAEA E A+K+AR + II Sbjct: 79 PSIELANLLTANSCFDRVFF------TNSGAEANEGAIKLARKWGKKNPNKAGQNRFEII 132 Query: 124 AFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFS 183 F+ FHGRTLAT++ +GK ++PG +P A+ ++ L S Sbjct: 133 TFNHSFHGRTLATMSASGKPGWDTIFAPQVPG------FPKAE-----------LNDLAS 175 Query: 184 VELAVED-VAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQR 242 VE + D A + EPVQGE G + F QALR + GIL+I+DE+QSG GRTG+ Sbjct: 176 VENLINDKTVAVMLEPVQGESGVIPATREFMQALRELTKKHGILLIVDEVQSGMGRTGEL 235 Query: 243 FAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALAS 302 FA+ GIEPD++ L K I GG+PL A++ R+E+ A G GGTY+GNP+ A +A Sbjct: 236 FAYQLSGIEPDIMTLGKGIGGGVPLAALLAREEI-AVFEAGDQGGTYNGNPLMTAVGVAV 294 Query: 303 LAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPA 362 + + + Q++ + K + LS + +LT A G+E +G Sbjct: 295 IKTLLEPGFL-------QSV-----KDKGAYLSSELLKLT---AKHGLEGERGEGLLRAL 339 Query: 363 QLAK-----VMEAAR---ARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 +L K +++ AR GLLL + +++R + L + +++ + +L L + Sbjct: 340 KLGKDIGPQIVDIARDLNPVGLLL--NSPRPNLLRFMPSLNVTTAEIDQMIAMLSDVLTQ 397 Query: 415 L 415 L Sbjct: 398 L 398 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: 409 Number of extensions: 17 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: 400 Length adjustment: 31 Effective length of query: 385 Effective length of database: 369 Effective search space: 142065 Effective search space used: 142065 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