Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >FitnessBrowser__Dino:3609962 Length = 413 Score = 182 bits (462), Expect = 2e-50 Identities = 132/428 (30%), Positives = 216/428 (50%), Gaps = 32/428 (7%) Query: 6 ADLMARRTAAVPRGVGQIH--PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63 +DL+ RR + V + P+ + + D GR ++D + + GH HP++ Sbjct: 2 SDLLKRRARLMGPNVPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNNVP--HVGHCHPRV 59 Query: 64 IAAVTEQLNKL-THTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKI 122 + A+ Q L THT + +E ++ E++ + + LLV TGSEAV+ A+++ Sbjct: 60 VDAIARQARVLNTHTRY---LHEGVLDYIERLTGTMDNGL-DQALLVCTGSEAVDVALRM 115 Query: 123 ARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVP---YSAGMGLMPG---GIFRALYPNEL 176 ARAATG+ G+IA YHG T L+ + P YS + L+P G A + Sbjct: 116 ARAATGKTGLIATDNTYHGNTTAVAQLSTRRPPIGGYSDHVRLVPAPEPGTDGAAF---- 171 Query: 177 HGVSIDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGIL 236 G + + A +E +AA+I+ P+ G P+ F++ A G L Sbjct: 172 -GAHVARAAAELE------TAGHGVAALIVCPIFANEGLPCLPRGFLEPAVAALRTRGGL 224 Query: 237 LIADEVQTGAGRTG-TFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPG-G 294 LI+DEVQ G GR G F+ + +G+A D+ T KS+ G+P+AGV + E M A G Sbjct: 225 LISDEVQPGFGRLGDVFWGYQALGIAPDVVTLGKSMGNGYPVAGVVARTEIMGAFREAFG 284 Query: 295 LGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGA 354 T+ GSP+A AAA+AV++V E+E L++ K VG + L+A+ ++P I VR G Sbjct: 285 YFNTFGGSPVAAAAAMAVLDVLEDEGLVENAKRVGRYTLERLQAL--RHPAIDGVRGYGL 342 Query: 355 MIAVELFENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKG 414 A++L + + PN A A V +A+ + +++ G ++L++ PL E D+ Sbjct: 343 AFALDLVDTDGA--PNTALAAAVTEEAKRRSVLINRIGRDMHILKIRPPLPFAPEHGDRL 400 Query: 415 LAILEECF 422 +L+ F Sbjct: 401 GDVLQAAF 408 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: 439 Number of extensions: 24 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: 425 Length of database: 413 Length adjustment: 32 Effective length of query: 393 Effective length of database: 381 Effective search space: 149733 Effective search space used: 149733 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