Align primary-amine oxidase (EC 1.4.3.21) (characterized)
to candidate WP_011652550.1 RL_RS15680 primary-amine oxidase
Query= BRENDA::A1R2C3 (656 letters) >NCBI__GCF_000009265.1:WP_011652550.1 Length = 662 Score = 560 bits (1443), Expect = e-164 Identities = 298/628 (47%), Positives = 389/628 (61%), Gaps = 10/628 (1%) Query: 19 HPLEQLSAHEIHQARRILADAGLVAETTRFAYLGLIEPPKAVFQADAAD--APRLVRAML 76 HPL+ LS EI A IL D +A T RF L EP KA A PRL + Sbjct: 9 HPLDPLSLDEIASAVAILKDTQTLAATFRFPITRLEEPTKADLAAYRLGDRLPRLAFILA 68 Query: 77 WDAAQSRSLDVRLSLATGLVLD--QRELNPEIDGQLPVLLEEFGIIEDILAVDPQWNAAL 134 D + + + + L G V + L+ GQ P++L EF +E + DP+W AA+ Sbjct: 69 IDISNGETFEGIVDLTAGTVSSYIRLPLDELPYGQPPIMLCEFETVEGTVKSDPRWIAAV 128 Query: 135 ASRGLTPAQV---RVAPLSAGVFEYGNEEGKRLLRGLGFRQDHPADHPWAHPIDGLVAFV 191 RG+T + ++ P S+G F E+GKR++R + + ++ D+ +AHPI+G+VA V Sbjct: 129 KKRGITDEDIPLIQIDPFSSGYFGREFEKGKRIVRAVSYWREDVRDNGYAHPIEGVVAVV 188 Query: 192 DIENRRVNHLIDDGPV-PVPEVNGNYTDPTIHGELRTDLKPIEITQPEGPSFTLEGNHLS 250 D+ RV L+DD + PVP+ NY T E R DL P+ I QP+GPSFT++G + Sbjct: 189 DLITNRVVDLVDDEKIIPVPKKKRNYGRETFP-EQRPDLTPLHIVQPQGPSFTVDGWKVE 247 Query: 251 WAGWDLRVGFDAREGLVLHQLHHSHQGRRRPVVHRASISEMVVPYGDPSPYRSWQNYFDS 310 W W RVGF REGLVLH+L QGR RPVV RAS++EMVVPY DP+ W++ FD+ Sbjct: 248 WQNWSFRVGFTPREGLVLHELGIKDQGRLRPVVFRASVTEMVVPYADPTANHYWKSAFDA 307 Query: 311 GEYLVGRDANSLKLGCDCLGDITYMSPVVADDFGNPRVIENGICIHEEDAGILWKHTDEW 370 GEY +GR AN L+LGCDCLG I Y ADD G P +++N IC+HEED GILWKH + Sbjct: 308 GEYGLGRLANCLELGCDCLGHIHYFDVPAADDLGQPFIMKNAICMHEEDYGILWKHYEFR 367 Query: 371 AGSNEVRRNRRLVVSFFTTVGNYDYGFYWYLYLDGTIEFEAKATGIVFTAAL-PDKDYAY 429 G EVRR+RRLV+SFF TVGNYDYGFYWYLY DGTI+ EAK TGI+ TAA+ + Y + Sbjct: 368 NGIFEVRRSRRLVISFFATVGNYDYGFYWYLYQDGTIQLEAKLTGIIQTAAVATGETYPW 427 Query: 430 ASEIAPGLGAPYHQHLFSARLDMMVDGGTNRVEELDLVRLPKGPGNPHGNAFTQKRTVLT 489 + LG P HQH F+ARL M VDGG N V E + V P G NP+GN F + VL Sbjct: 428 GGMVDDNLGGPTHQHFFNARLHMDVDGGDNTVTEHEFVPRPWGEDNPYGNVFDTRSRVLK 487 Query: 490 RESEAVRDADGTKGRVWHISNPDSLNHLGHPVGYTLYPEGNPTLAMADDSSIASRAAFAK 549 RE ++ A+G GR W +SNP+ N +G GY + +P + DS++A R FAK Sbjct: 488 RELDSPAVANGETGRYWKVSNPNIKNSVGKAPGYKIVVMPSPVMLAQPDSTVAQRGGFAK 547 Query: 550 HHLWVTQHAEDELYAAGDFVNQHPGGAGLPSYVAQDRDIDGQDLVVWHSFGLTHFPRPED 609 H+WVT E YA+GD+ N H GG GLP YV Q+RDI+ D+V+WHSFG TH +PED Sbjct: 548 KHIWVTAFDAREKYASGDYPNVHAGGDGLPGYVKQNRDIENADVVLWHSFGHTHVCKPED 607 Query: 610 WPIMPVDTTGFTLKPHGFFDQNPTLNVP 637 +PIMPV+ GFTLKP+GFF N +++P Sbjct: 608 FPIMPVEYAGFTLKPNGFFASNIAMDLP 635 Lambda K H 0.319 0.137 0.432 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: 1383 Number of extensions: 82 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: 656 Length of database: 662 Length adjustment: 38 Effective length of query: 618 Effective length of database: 624 Effective search space: 385632 Effective search space used: 385632 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 (21.7 bits) S2: 54 (25.4 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