Align Primary amine oxidase 1; AtAO1; EC 1.4.3.21 (characterized)
to candidate PfGW456L13_2439 Monoamine oxidase (1.4.3.4)
Query= SwissProt::O23349 (650 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2439 Length = 762 Score = 288 bits (738), Expect = 5e-82 Identities = 202/648 (31%), Positives = 303/648 (46%), Gaps = 42/648 (6%) Query: 23 HPLDPLTPQEINKTSFIVKKSHLGNLKD-LTFHYLDLEEPNKSHVLQWLSPNPSKKPPPP 81 +PL+PL+ EI IVKKS N K F + ++EP K V + + P Sbjct: 130 NPLNPLSAAEITTAVDIVKKSE--NYKPGFRFTEVSVKEPPKDQVWNFALTGQNVAQP-- 185 Query: 82 RRRSFVVVRAGGQTYELIIDLTTSKIASSRIYTG-HGFPSFTFIELFKASKLPL-TYPPF 139 R++ +VV G E +DL T ++ S + G HG ++ F + + T P + Sbjct: 186 -RQASIVVLDGKHVIEAQVDLDTKELKSWKPIEGAHGM---VLLDDFATVQTAVETSPEY 241 Query: 140 KKSILDRSLN-ISEVSCIPFTVGWY----GETTTRRELKASCFYRDGSVNVFTRPIEGIT 194 +++ R +N + +V P TVG++ G +R LK + G N + PIEG+ Sbjct: 242 AQALAKRGINDVKKVVATPLTVGFFDGKDGLAQDKRLLKIVSYLNTGDGNYWAHPIEGLV 301 Query: 195 VTIDVDSMQVIKYSDRFRKPIP-DKEGNDFRTKH----RPFPFFCNVSDTGFKILGNRVK 249 +D++ ++IK D P+P + D R + +P + I GN + Sbjct: 302 AIVDLEQKKLIKIEDDALIPVPMNPTPYDGRGRQGVAVKPLEII-EPEGKNYTISGNSIH 360 Query: 250 WANWKFHVGFTARAGVTISTASVLDPRTKRFRRVMYRGHVSETFVPYMDPTYEWYYRTFM 309 W NW FHV +R G +ST + D KR ++MY G + VPY DP WY++ ++ Sbjct: 361 WQNWDFHVRLDSRVGPILSTVTYDDKGKKR--KIMYEGSLGGMIVPYGDPDVGWYFKAYL 418 Query: 310 DIGEFGFGRSAVNLQPLIDCPQNAAFLDGHVAGPDGTAQKMTNVMCVFEKNGYGASFRHT 369 D G++G G + D PQNA LD +A GT + M VFE+ G ++H Sbjct: 419 DSGDYGMGTLTSPIARGKDAPQNAVLLDATIADYTGTPTAIPRAMAVFERYA-GPEYKHQ 477 Query: 370 EINVPGQVITSGEAEISLVVRMVATLGNYDYIVDWEFKKNGAIRVGVDLTGVLEVKATSY 429 E+ P E LVVR ++T+GNYDYI DW F++NG I + TG+ VK Sbjct: 478 EMGQPNLSTERRE----LVVRWISTVGNYDYIFDWVFQQNGTIGIDAGATGIEAVKGVKS 533 Query: 430 TSNDQIT---ENVYGTLVAKNTIAVNHDHYLTYYLDLDVDGNGNSLVKAKLKTVRVTEVN 486 + + T + YGTL+ N + H H + LD+DVDG NSLV+ V N Sbjct: 534 KTMHEDTAREDTRYGTLLDHNIVGTTHQHIYNFRLDMDVDGEQNSLVEVN----PVVLPN 589 Query: 487 KTSSRRKSYWTVVKETAKTEADGRVRLGSDPVELLIVNPNKKTKIGNTVGYRLIP----- 541 R S + E + V LL N +K+ K+GN V Y+LIP Sbjct: 590 DRGGPRTSTMQTETKVVGNEQQAAQKFDPSTVRLL-TNFSKENKVGNPVSYQLIPYAGGT 648 Query: 542 EHLQATSLLTDDDYPELRAGYTKYPVWVTAYDRSERWAGGFYSDRSRGDDGLAVWSSRNR 601 + + D++ R + +WVT Y+ E++ G Y +RS D GL ++ N Sbjct: 649 HPVAKGANFGKDEWLYHRLSFMDKQLWVTQYNPEEKYPEGKYPNRSDKDSGLGQFTQDNH 708 Query: 602 EIENKDIVMWYNVGFHHIPYQEDFPVMPTLHGGFTLRPSNFFDNDPLI 649 IEN D V+W G HI E++P+MPT L+P NFFD P + Sbjct: 709 SIENTDDVVWLTTGTTHIARAEEWPIMPTEWVHVLLKPWNFFDETPTL 756 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: 1273 Number of extensions: 69 Number of successful extensions: 9 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: 762 Length adjustment: 39 Effective length of query: 611 Effective length of database: 723 Effective search space: 441753 Effective search space used: 441753 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