Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 7025922 Shewana3_3071 glutamate-1-semialdehyde aminotransferase (RefSeq)
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__ANA3:7025922 Length = 430 Score = 143 bits (361), Expect = 9e-39 Identities = 103/301 (34%), Positives = 152/301 (50%), Gaps = 17/301 (5%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P+ + A ++D DGK YID+VG G + LGH +P + EA+ A + AP Sbjct: 33 PLFIEKADGAYIYDADGKAYIDYVGSWGPMILGHNHPKIREAVLAAVHNGLSFG---APT 89 Query: 75 GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTL 134 + + E++ VP + + +SG EA +A+++ARG T + I+ F+G +HG Sbjct: 90 ELEVQMAEKVIAMVPSIEQVR--MVSSGTEATMSAIRLARGFTNRDKILKFEGCYHGHAD 147 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCE-QALKAMDRLFSVELAVEDVAA 193 L G A +G+ P +P A +T L ++ LF E +++ Sbjct: 148 CLLVKAGSGA---LTLGQPSSP--GIPEDFAKHTLTAVYNDLDSVRSLF--EQYPTEISC 200 Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253 I EPV G + P F + LR CDE G L+IIDE+ +GF R + A G+ PD Sbjct: 201 IIIEPVAGNMNCIPPIPGFLEGLRAMCDEFGALLIIDEVMTGF-RVSRSGAQGHYGVTPD 259 Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGG---LGGTYSGNPISCAAALASLAQMTDEN 310 L L K I GGMP+GA GRKE+M + G GT SGNPI+ +A LA + + +E Sbjct: 260 LTTLGKVIGGGMPVGAFGGRKEVMQFIAPTGPVYQAGTLSGNPIAMSAGLAQMEALCEEG 319 Query: 311 L 311 L Sbjct: 320 L 320 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: 449 Number of extensions: 27 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: 430 Length adjustment: 32 Effective length of query: 384 Effective length of database: 398 Effective search space: 152832 Effective search space used: 152832 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