Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__azobra:AZOBR_RS19630 Length = 428 Score = 357 bits (916), Expect = e-103 Identities = 185/413 (44%), Positives = 256/413 (61%), Gaps = 2/413 (0%) Query: 5 SISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL 64 ++ + +A P+ + NAE+WD +G R+IDF GGI VLN GH +P ++EA++AQ R Sbjct: 13 AVPRGLANAMPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRF 72 Query: 65 THYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIA 124 TH P+ ++ L E+L+ VP S P +GAEA ENA+K+AR TG+ +IA Sbjct: 73 THTCAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIARAHTGRPGVIA 132 Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184 F G FHGRTL + L GKV PYK G P VYH P+P+A GV+ + +LKA+++LF Sbjct: 133 FSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDSLKALEQLFKS 192 Query: 185 ELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244 ++ VAA I EPVQGEGGF P F QALR+ CDE GIL+IIDEIQ+GF RTG+ FA Sbjct: 193 DVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGKMFA 252 Query: 245 FPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLA 304 G+EPDL+ +AKS+AGG PL AV G+ E+M A GG+GGTY+G+P++ AALA L Sbjct: 253 IEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGSPLATTAALAVLD 312 Query: 305 QMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAP-AQ 363 + +E L + I R+ IG + +G M +E G+ P A+ Sbjct: 313 VIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTKEPAAE 372 Query: 364 LAKVMEA-ARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415 L K + A A +GL+L+ G ++IR+L PLT +++EGLDI+E+ L EL Sbjct: 373 LTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERSLEEL 425 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: 518 Number of extensions: 14 Number of successful extensions: 2 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: 428 Length adjustment: 32 Effective length of query: 384 Effective length of database: 396 Effective search space: 152064 Effective search space used: 152064 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