Align Arginine 2-monooxygenase (Decarboxylating); EC 1.13.12.3; SubName: Full=FAD-dependent oxidoreductase (characterized, see rationale)
to candidate AO356_14230 AO356_14230 amine oxidase
Query= uniprot:A0A291T0Y3 (569 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_14230 Length = 560 Score = 716 bits (1848), Expect = 0.0 Identities = 325/552 (58%), Positives = 426/552 (77%), Gaps = 3/552 (0%) Query: 19 DALPPVTMFGPDFPYAYDDYLAHPAGLGQIPATEHGSEVAVVGGGLSGVVTAYELMKMGL 78 D P+T+FGPDFP+A+DD++ HPAGLG IPA HG+EVA+VG G++G+V AYELMK+GL Sbjct: 10 DGKKPITIFGPDFPFAFDDWIEHPAGLGSIPAHNHGTEVAIVGAGIAGLVAAYELMKLGL 69 Query: 79 RPVVYEADRIGGRLRTVGFDGCDDSLTAEMGAMRFPPSSTALQHYIDLVGLKTRPFPNPL 138 +PVVYEA ++GGRLR+ F+G + + AE+G MRFP SSTA HY+D +GL+T+PFPNPL Sbjct: 70 KPVVYEASKMGGRLRSQAFNGAE-GVIAELGGMRFPVSSTAFYHYVDKLGLETKPFPNPL 128 Query: 139 APDTPSTVVDLKGESHYARTIDDLPPVYREVADAWSACLEEGADFSDMNRAIRERDVPRI 198 P + STV+DL+G+++YA+ + DLP +++EVADAW+ LE+G+ F D+ +AIR+RDVPR+ Sbjct: 129 TPASGSTVIDLEGQTYYAQKLADLPALFQEVADAWADALEDGSRFGDIQQAIRDRDVPRL 188 Query: 199 REIWSRLVEKLDNQTFYGFLCDSTAFT--SFRHREIFGQVGFGTGGWDTDFPNSILEILR 256 +E+W+ LV D++TFY F+ S AF SF+HRE+FGQVGFGTGGWD+DFPNS+LEI R Sbjct: 189 KELWNTLVPLWDDRTFYDFVATSKAFAKLSFQHREVFGQVGFGTGGWDSDFPNSMLEIFR 248 Query: 257 VVYTEADDHHRGIVGGSQQLPLRLWEREPGKIVHWPQGTSLASLHGGAPRPAATRLHRAA 316 VV T DDH +VGG +Q+P +W P + HWP+GTSL SLH GAPR R+ R+A Sbjct: 249 VVMTNCDDHQHLVVGGVEQVPHGIWNHVPERCAHWPEGTSLNSLHLGAPRSGVKRIARSA 308 Query: 317 GDRVVVTDASGDIRSYRAVVFTAQSWMLLSQIDCDDSLFPIDHWTAIERTHYMESSKLFV 376 R VTD + R Y AV+ T QSW+L +QI+C+++LF W A++RT YM+SSK FV Sbjct: 309 DGRFSVTDVWENTREYAAVLVTCQSWLLTTQIECEEALFSQKMWMALDRTRYMQSSKTFV 368 Query: 377 PVDRPFWLDEDETTGRDTMSMTLTDRMTRGTYLLDDGPDRPAVICLSYTWCDDSLKWLPL 436 VDRPFW D+D TGRD MSMTLTDR+TRGTYL D+G D+P VICLSY+W D+LK LP Sbjct: 369 MVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGVICLSYSWMSDALKMLPH 428 Query: 437 SANERMEVMLKSLSEIYPNVDIRKHIIGSPITVSWENEPYFMGAFKANLPGHYRYQRRLF 496 +R+++ L +L +IYP VDI IIG PITVSWE +P+F+GAFK LPGHYRY +R++ Sbjct: 429 PVEKRVKLALDALKKIYPKVDIAARIIGDPITVSWEADPHFLGAFKGALPGHYRYNQRMY 488 Query: 497 THFMQDRLPADKRGVFLAGDDISWTAGWAEGAVQTALNAVWGVMHRFGGATDPKNPGPGD 556 HFMQD +PA++RG+F+AGDD+SWT W EGAVQT+LNAVWG+M FGG T +NPGPGD Sbjct: 489 AHFMQDDMPAEQRGIFIAGDDVSWTPAWVEGAVQTSLNAVWGIMKHFGGETHAENPGPGD 548 Query: 557 LYEEIAPVELPE 568 ++ EI P+ LPE Sbjct: 549 VFHEIGPIALPE 560 Lambda K H 0.320 0.138 0.436 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: 1117 Number of extensions: 44 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: 569 Length of database: 560 Length adjustment: 36 Effective length of query: 533 Effective length of database: 524 Effective search space: 279292 Effective search space used: 279292 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