Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate N515DRAFT_3307 N515DRAFT_3307 glutamate-1-semialdehyde 2,1-aminomutase
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Dyella79:N515DRAFT_3307 Length = 426 Score = 149 bits (376), Expect = 2e-40 Identities = 107/293 (36%), Positives = 149/293 (50%), Gaps = 17/293 (5%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74 P + A +WD +GKRYID+VG G + +GH +P V EA++ + P Sbjct: 32 PFFTARADGAYLWDVEGKRYIDYVGSWGPMIVGHNHPRVREAVERAVKDGLSF---GTPC 88 Query: 75 GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTL 134 + + E +++ VP S + M+ NSG EA +A+++ARGATG+ I+ F+G +HG Sbjct: 89 PAEITMAETITRLVP-SVDMVRMV-NSGTEATMSAIRLARGATGRSKIVKFEGCYHGHGD 146 Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVT-CEQALKAMDRLFSVELAVEDVAA 193 + L G A V PG +P +AD +T L A + LF+ A D+A Sbjct: 147 SFLVKAGSGA-LTFGVPTSPG----VPKAAADLTLTLAYNDLAAAEALFAEHGA--DIAG 199 Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253 I EPV G + + Q LR C G L+I DE+ +GF R A GI PD Sbjct: 200 LIIEPVAGNMNCIPPKDGYLQGLRALCTRHGALLIFDEVMTGF-RVALGGAQAHYGITPD 258 Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGG---LGGTYSGNPISCAAALASL 303 L K I GGMP+GA GR+ELM + G GT SGNP++ AA LA L Sbjct: 259 LSTFGKIIGGGMPVGAYGGRRELMEQIAPAGPIYQAGTLSGNPVAMAAGLAML 311 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: 466 Number of extensions: 32 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: 426 Length adjustment: 32 Effective length of query: 384 Effective length of database: 394 Effective search space: 151296 Effective search space used: 151296 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