Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_128083232.1 CAter10_RS21330 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_001584165.1:WP_128083232.1 Length = 420 Score = 347 bits (890), Expect = e-100 Identities = 185/410 (45%), Positives = 253/410 (61%), Gaps = 11/410 (2%) Query: 8 QSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY 67 + + ++ SH N+E+WD +G+R+IDF GI VLN GH +P +V AIQ Q + TH Sbjct: 11 RGVGVMCDFYASHALNSEIWDVEGRRFIDFAAGIAVLNTGHRHPKLVAAIQEQLGKFTHT 70 Query: 68 AFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDG 127 A+ P+G Y+ L E+++ P + ++GAEA ENA+K+AR ATG+ A+IAF G Sbjct: 71 AYQIVPYGSYVELAERINAVTPGDHAKKTTFFSTGAEAVENAVKIARAATGRSAVIAFSG 130 Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187 FHGRT+ + L GKV PYK G P VYH+P+P GV+ E +L A+ LF ++ Sbjct: 131 AFHGRTMMGMALTGKVVPYKVGFGPFPAEVYHVPFPVELHGVSIENSLAALQSLFKADVD 190 Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247 + VAA I EPVQGEGGF A PAF QALR+ CDE GIL+++DE+Q+GF RTG+ FA Sbjct: 191 PKRVAAIILEPVQGEGGFYAAPPAFMQALRKLCDEHGILLVVDEVQTGFARTGKLFAVEH 250 Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT 307 G+ PDL+ +AKS+AGGMPL AV GR E+M A GGLGGTY+GNP++ A+ALA L + Sbjct: 251 SGVIPDLMTMAKSLAGGMPLSAVCGRAEIMDAAAPGGLGGTYAGNPLAVASALAVLDVIE 310 Query: 308 DENLA----TWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ 363 +E L G R +Q + E +A P I + G+GAM +EF A Sbjct: 311 EEKLVERANVLGGRLKQVL----EGLRAD--VPQIADIRGLGAMVAVEFTQPGSKQPDAD 364 Query: 364 LAKVMEA-ARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 K ++A A GLLL+ G + IR L PLTIE +++E L IL + + Sbjct: 365 FTKKVQAEALKNGLLLLSCGVYSNAIRFLFPLTIEDALMDEALAILSKAM 414 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: 508 Number of extensions: 21 Number of successful extensions: 3 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: 420 Length adjustment: 32 Effective length of query: 384 Effective length of database: 388 Effective search space: 148992 Effective search space used: 148992 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