Align Lysine 2-monooxygenase (EC 1.13.12.2) (characterized)
to candidate GFF5058 PS417_25910 amine oxidase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1171 (560 letters) >FitnessBrowser__WCS417:GFF5058 Length = 560 Score = 1112 bits (2876), Expect = 0.0 Identities = 531/560 (94%), Positives = 541/560 (96%) Query: 1 MNKNNRHPADGKKPVTIFGPDFPFAFDDWIEHPAGLGSIPEHNHGAEVAIVGGGIAGLVA 60 M+K NRHPADGKKP+TIFGPDFPFAFDDWIEHPAGLGSIP NHGAEVAIVG GIAGLVA Sbjct: 1 MSKTNRHPADGKKPITIFGPDFPFAFDDWIEHPAGLGSIPTANHGAEVAIVGAGIAGLVA 60 Query: 61 AYELMKLGLKPVVYEASKMGGRLRSQAFNGAEGIVAELGGMRFPVSSTAFYHYVDKLGLE 120 AYELMKLGLKPVVYEASKMGGRLRSQAF GAEGI+AELGGMRFPVSSTAFYHYVDKLGLE Sbjct: 61 AYELMKLGLKPVVYEASKMGGRLRSQAFEGAEGIIAELGGMRFPVSSTAFYHYVDKLGLE 120 Query: 121 TKPFPNPLTPASGSTVIDLEGQTHYAQKLSDLPALFQEVADAWADALEAGSQFSDIQQAI 180 TKPFPNPLTPASGSTVIDLEGQTHYAQKLSDLP LFQEVADAWADALEAGSQF DIQQAI Sbjct: 121 TKPFPNPLTPASGSTVIDLEGQTHYAQKLSDLPVLFQEVADAWADALEAGSQFGDIQQAI 180 Query: 181 RDRDVPRLKELWNTLVPLWDDRTFYDFVATSKAFAKLSFHHREVFGQVGFGTGGWDSDFP 240 RDRDVPRLKELWN LVPLWDDRTFYDFVATSKAFAKLSFHHREVFGQVGFGTGGWDSDFP Sbjct: 181 RDRDVPRLKELWNKLVPLWDDRTFYDFVATSKAFAKLSFHHREVFGQVGFGTGGWDSDFP 240 Query: 241 NSMLEIFRVVMTNCDDHQHLVVGGVEQVPQGIWRHVPERCAHWPAGTSLSSLHNGAPRTG 300 NSMLEIFRVVMTNCDDHQHLVVGGV QVP GIWRHVPERCAHWPAGTSLSSLH GAPR G Sbjct: 241 NSMLEIFRVVMTNCDDHQHLVVGGVAQVPMGIWRHVPERCAHWPAGTSLSSLHRGAPRAG 300 Query: 301 VKKIAHAPGGRFAVTDNWGDTREYAAVLTTCQSWLLTTQIECDETLFSQKMWMALDRTRY 360 VK+IAHA GRFAVTDN+GDTREYAAVLTTCQSWLLTTQIECDETLFSQKMWMALDRTRY Sbjct: 301 VKRIAHAADGRFAVTDNYGDTREYAAVLTTCQSWLLTTQIECDETLFSQKMWMALDRTRY 360 Query: 361 MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS 420 MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS Sbjct: 361 MQSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMS 420 Query: 421 DALKMLPQPVEKRVKLALDALKKIYPKVDIAARIIGDPITVSWEADPHFLGAFKGALPGH 480 DALKMLPQP++KRVKLALDALKKIYPKVDI ARIIGDPITVSWEADPHFLGAFKGALPGH Sbjct: 421 DALKMLPQPIDKRVKLALDALKKIYPKVDIKARIIGDPITVSWEADPHFLGAFKGALPGH 480 Query: 481 YRYNQRMYAHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGATH 540 YRYNQRMYAHFMQ DMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIM HFGG+TH Sbjct: 481 YRYNQRMYAHFMQKDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMTHFGGSTH 540 Query: 541 AENPGPGDVFNEIGPIALPE 560 ENPGPGDVF+EIGPIAL + Sbjct: 541 PENPGPGDVFDEIGPIALAD 560 Lambda K H 0.320 0.137 0.438 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: 1358 Number of extensions: 41 Number of successful extensions: 1 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: 560 Length of database: 560 Length adjustment: 36 Effective length of query: 524 Effective length of database: 524 Effective search space: 274576 Effective search space used: 274576 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: 53 (25.0 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