Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_007731008.1 C1M55_RS18665 diaminobutyrate--2-oxoglutarate transaminase
Query= reanno::pseudo3_N2E3:AO353_11510 (425 letters) >NCBI__GCF_002893965.1:WP_007731008.1 Length = 420 Score = 179 bits (454), Expect = 1e-49 Identities = 141/435 (32%), Positives = 218/435 (50%), Gaps = 37/435 (8%) Query: 1 MSKTNASLMKRREAAVPRGVGQIHPIFADHAKNSTVTDVEGREFIDFAGGIAVLNTGHLH 60 M+ AS+ + E+ V R + P A S + D GR+++DF G LN GH + Sbjct: 1 MNINEASIFETLESEV-RSYCRDWPAVFTSASGSWIRDENGRDYLDFFAGAGALNYGHNN 59 Query: 61 PKVIAAVTEQL--NKLTHTC-FQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVE 117 P + +A+ + + + +TH +A ++E ++ + G K TGS VE Sbjct: 60 PVLKSALVDYIMSDGITHGLDMSTVAKREFLETFQRNILEPRGLDYKVQFPGPTGSNTVE 119 Query: 118 NSIKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELH 177 ++K+AR TGR+ VI FT A+HG T+ L +TG + AG G+ + N Sbjct: 120 AALKLARKVTGRSAVINFTNAFHGMTLGALSVTGNSMK-RAGAGVPLVHTTPMPFDNYFD 178 Query: 178 GVS---------IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRA 228 GV+ +DDS + I R AA+I+E VQGEGG VA E+++ L Sbjct: 179 GVTEDFQWFSRVLDDSGSGINRP----------AAVIVETVQGEGGVNVARPEWLRALAT 228 Query: 229 LCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAG-GFPLAGVCGKAEYM 287 LC GILLI D+VQ G GRTG FF+ E+ G+ D+ T +KSI+G G P+A K E + Sbjct: 229 LCSDRGILLIVDDVQMGCGRTGPFFSFEEAGIVPDIVTLSKSISGYGMPMALTLFKRE-L 287 Query: 288 DAIAPGGLGGTYAG-SPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVI 346 D PG GT+ G +P + +A+ + ++ L G R+ + ++P Sbjct: 288 DVWGPGEHNGTFRGNNPAFVTSKVALDHYWSDDALTKTTLKKGARISECFANLSDQFP-- 345 Query: 347 GEVRALG-AMIAVELFENGDSHKPNAAAVAKVVAKARDKGLILLSCGTYGNVLRVLVPLT 405 GEV G ++ +FE +P A KV A D+GL+ + G V+++L LT Sbjct: 346 GEVSHRGRGLVQGLVFE-----QPERA--GKVCQLAFDEGLLAETSGPSDQVVKLLPALT 398 Query: 406 APDEQLDKGLAIMEE 420 D++L+ GL+I+ E Sbjct: 399 ITDDELEHGLSILAE 413 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: 428 Number of extensions: 18 Number of successful extensions: 4 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: 420 Length adjustment: 32 Effective length of query: 393 Effective length of database: 388 Effective search space: 152484 Effective search space used: 152484 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 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