Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_028311050.1 H566_RS0108125 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >NCBI__GCF_000482785.1:WP_028311050.1 Length = 435 Score = 469 bits (1206), Expect = e-137 Identities = 228/418 (54%), Positives = 307/418 (73%), Gaps = 3/418 (0%) Query: 4 TNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63 TNAD +ARR AA+PRGVGQ HP+ A+ A NA V DVEG+ +IDF GIAV+NTGH +P++ Sbjct: 7 TNADQLARRAAALPRGVGQAHPVVAQRALNAEVWDVEGKRYIDFVAGIAVVNTGHNNPRV 66 Query: 64 IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA 123 +AAV EQ+ THTCFQVLAY+ Y+ L EK+NA++PG AKK+ + +G+EAVENA+K+A Sbjct: 67 LAAVQEQMQHFTHTCFQVLAYDGYITLAEKLNARMPGPGAKKSFFMNSGAEAVENAIKVA 126 Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183 RAATGR G+IAF G +HGRTM TLGLTGKV PY G G ++ A +PN LHG+S +D Sbjct: 127 RAATGRPGIIAFNGGFHGRTMFTLGLTGKVDPYKIGFGPFSADVYHAPFPNPLHGLSAED 186 Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243 ++ +E +FK D E +AA IIEPVQGEGG+ AP F++ LR + D+HGIL+IADE+Q Sbjct: 187 ALKGVEALFKFDIEASRVAAFIIEPVQGEGGYLPAPAPFLRGLREIADRHGILIIADEIQ 246 Query: 244 TGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303 +G RTG F+ +E GVA D+ T AK + GGFP+A V G+AE MDA APGGLGGTY G+P Sbjct: 247 SGVCRTGKFYGIEHSGVAPDIITMAKGLGGGFPIAAVVGRAEVMDAAAPGGLGGTYGGNP 306 Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYP-VIGDVRALGAMIAVEL-F 361 ++CAAALAV+++ E+E L ++ +A G ++A L I +P + +VR LGAM+A+E Sbjct: 307 LSCAAALAVLDIVEDEQLNEKVQATGRTMLAKLDEIAAAHPDRVAEVRGLGAMLAIEFGT 366 Query: 362 ENGDSH-KPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAIL 418 + D H P+ A V +VA+AR +GL++LSCG YGNV+R++ PLT + L +GL +L Sbjct: 367 RDADGHWTPDGALVKAIVAEARARGLLILSCGPYGNVIRLMPPLTVGEAVLAEGLDLL 424 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: 570 Number of extensions: 23 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: 425 Length of database: 435 Length adjustment: 32 Effective length of query: 393 Effective length of database: 403 Effective search space: 158379 Effective search space used: 158379 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: 51 (24.3 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