Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase
Query= reanno::pseudo3_N2E3:AO353_11510 (425 letters) >FitnessBrowser__azobra:AZOBR_RS19590 Length = 405 Score = 182 bits (463), Expect = 1e-50 Identities = 123/395 (31%), Positives = 194/395 (49%), Gaps = 52/395 (13%) Query: 36 VTDVEGREFIDFAGGIAVLNTGHLHPKVIAAVTEQLNKLTHTCFQVLAYEPYVELCEKIN 95 V D EG ++D + +N GH HPK++ A+ +Q +KLT T + + E++ Sbjct: 35 VWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQQASKLTLTS-RAFRNDQLALFYEELA 93 Query: 96 AKVPGDFAKKTLLVTTGSEAVENSIKIAR--------AATGRAGVIAFTGAYHGRTMMTL 147 A + K L + +G+EAVE++IK R +A +I + +HGRT+ + Sbjct: 94 ALTG---SHKILPMNSGAEAVESAIKTVRKWGYEVRGVPENQAEIIVCSDNFHGRTISIV 150 Query: 148 GLT------GKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEPRDI 201 + G P++ G +P G AL A + Sbjct: 151 SFSTDPDARGGFGPFTPGFRTVPFGDAAAL----------------------EAALTPNT 188 Query: 202 AAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVA 261 A+++EP+QGE G + P +++R+R LC + +++I DE+QTG GRTG A E GV Sbjct: 189 VAVLLEPIQGEAGVVIPPAGYLRRVRDLCTERNVVMILDEIQTGLGRTGKLLAEEHEGVE 248 Query: 262 ADLTTFAKSIAGGF-PLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEH 320 AD+T K+++GGF P++ V +E + + PG G T+ G+P+ACA A A M V EE Sbjct: 249 ADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAAMRVLVEEG 308 Query: 321 LLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAAAVAKVVAK 380 ++D A G + L AI++ VI E R G M+AVEL P A + Sbjct: 309 MIDNAAAQGAYFLEQLGAIRSN--VIREARGRGLMLAVEL-------HPEAGGARRYCEA 359 Query: 381 ARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGL 415 R +G +L+ T+ + +R+ PL EQ+D L Sbjct: 360 LRARG--VLAKDTHDHTIRIAPPLVITREQVDWAL 392 Lambda K H 0.320 0.137 0.395 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: 406 Number of extensions: 24 Number of successful extensions: 6 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: 425 Length of database: 405 Length adjustment: 31 Effective length of query: 394 Effective length of database: 374 Effective search space: 147356 Effective search space used: 147356 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