Align Primary amine oxidase 1; AtAO1; EC 1.4.3.21 (characterized)
to candidate BWI76_RS13080 BWI76_RS13080 tyramine oxidase
Query= SwissProt::O23349 (650 letters) >FitnessBrowser__Koxy:BWI76_RS13080 Length = 752 Score = 264 bits (675), Expect = 1e-74 Identities = 197/654 (30%), Positives = 301/654 (46%), Gaps = 52/654 (7%) Query: 23 HPLDPLTPQEINKTSFIVKKSHLGNLKDLT-FHYLDLEEPNKSHVLQW-LSPNPSKKPPP 80 HPL+ L+ EI+ IVK + + K T F + L EP+K V + L+ P P Sbjct: 121 HPLNSLSAAEISAAVAIVKAA--ADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAP-- 176 Query: 81 PRRRSFVVVRAGGQTYELIIDLTTSKIAS-SRIYTGHGF---PSFTFIELFKASKLPLTY 136 R + V++ G E ++DL K+ S + I HG F ++ + Sbjct: 177 --RTADVIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAE 234 Query: 137 PPFKKSILDRSLNISEVSCIPFTVGWY----GETTTRRELKASCFYRDGSVNVFTRPIEG 192 K I D S +V P TVG++ G R LK + G N + PIE Sbjct: 235 VLKKHGIDDPS----KVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIEN 290 Query: 193 ITVTIDVDSMQVIKYSDRFRKPIPDKEGNDFRTKHRPFPF-----FCNVSDTGFKILGNR 247 + +D++ ++IK + P+P + + R P + I G+ Sbjct: 291 LVAVVDLEQKKIIKIEEGPTIPVP-MAARPYDGRDRVAPTVKPLEIIEPEGKNYTITGDM 349 Query: 248 VKWANWKFHVGFTARAGVTISTASVLDPRTKRFRRVMYRGHVSETFVPYMDPTYEWYYRT 307 + W NW FH+ +R G +ST + D KR +VMY G + VPY DP WY++ Sbjct: 350 IHWRNWDFHLRMNSRVGPILSTVTWNDNGKKR--QVMYEGSLGGMIVPYGDPDVGWYFKA 407 Query: 308 FMDIGEFGFGRSAVNLQPLIDCPQNAAFLDGHVAGPDGTAQKMTNVMCVFEKNGYGASFR 367 ++D G++G G + D P NA LD +A GT + + +FE+ G ++ Sbjct: 408 YLDSGDYGMGTLTSPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYA-GPEYK 466 Query: 368 HTEINVPGQVITSGEAEISLVVRMVATLGNYDYIVDWEFKKNGAIRVGVDLTGVLEVKAT 427 H E+ P E LVVR ++T+GNYDYI DW F +NG I + TG+ VK Sbjct: 467 HLEMGKPNVSTERRE----LVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGV 522 Query: 428 -SYTSNDQIT--ENVYGTLVAKNTIAVNHDHYLTYYLDLDVDGNGNSLVKAKLKTVRVTE 484 + T +D + YGTL+ N + H H + LDLDVDG N+LV + T Sbjct: 523 QAKTMHDPSAKEDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTA 582 Query: 485 VN-KTSSRRKSYWTVVKE--TAKTEADGRVRLGSDPVELLIVNPNKKTKIGNTVGYRLIP 541 +TS+ + + +T+ E A+ G +RL S N K+ ++GN V Y++IP Sbjct: 583 GGPRTSTMQINQYTIASEQKAAQKFDPGTIRLLS--------NTTKENRMGNPVSYQIIP 634 Query: 542 ----EHLQATSL-LTDDDYPELRAGYTKYPVWVTAYDRSERWAGGFYSDRSRGDDGLAVW 596 H AT D++ R + +WVT Y +ER+ G Y +RS D GL + Sbjct: 635 YAGGTHPVATGAKFAPDEWIYHRLSFMDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQY 694 Query: 597 SSRNREIENKDIVMWYNVGFHHIPYQEDFPVMPTLHGGFTLRPSNFFDNDPLIG 650 + + ++N D V+W G H+ E++P+MPT L+P NFFD P +G Sbjct: 695 AKDDESLDNHDDVVWITTGTTHVARAEEWPIMPTEWAHALLKPWNFFDETPTLG 748 Lambda K H 0.320 0.138 0.424 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: 1260 Number of extensions: 58 Number of successful extensions: 8 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: 650 Length of database: 752 Length adjustment: 39 Effective length of query: 611 Effective length of database: 713 Effective search space: 435643 Effective search space used: 435643 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: 54 (25.4 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