Align Primary amine oxidase 1; AtAO1; EC 1.4.3.21 (characterized)
to candidate HSERO_RS17625 HSERO_RS17625 tyramine oxidase
Query= SwissProt::O23349 (650 letters) >FitnessBrowser__HerbieS:HSERO_RS17625 Length = 748 Score = 291 bits (745), Expect = 7e-83 Identities = 199/647 (30%), Positives = 301/647 (46%), Gaps = 37/647 (5%) Query: 23 HPLDPLTPQEINKTSFIVKKSHLGNLKDLTFHYLDLEEPNKSHVLQWLSPNPSKKPPPPR 82 HPL+PL+ EIN ++K S + F + L EP K V W + R Sbjct: 115 HPLNPLSADEINAALEVLKASGRWQ-PNYRFTEITLAEPPKEQV--WKFALGERGQTIAR 171 Query: 83 RRSFVVVRAGGQTYELIIDLTTSKIASSRIYTGHGFPSFTFIELFKASKLPL-TYPPFKK 141 R F ++ G + E +DL + +R G ++ F + + + P + + Sbjct: 172 RADFTLLD-GSKVIEGTVDLGQRNV--TRWEPKEGVHGMVLVDDFATVQNAMESSPEYAQ 228 Query: 142 SILDRSL-NISEVSCIPFTVGWYGETTTRRE----LKASCFYRDGSVNVFTRPIEGITVT 196 ++ R + +I +V P TVG++G +E LK + G N + PIE + Sbjct: 229 ALAKRGITDIKKVVATPLTVGYFGGKDALQEDARLLKVVSYLDVGDGNYWAHPIENLVAV 288 Query: 197 IDVDSMQVIKYSDRFRKPIPDK----EGNDFRTKHRPFPFFCNVSD-TGFKILGNRVKWA 251 +D+ +VIK D P+P K +G+ P P + + + I GN ++W Sbjct: 289 VDLVQKKVIKIEDNGVIPVPMKPTGYDGSGRALVPPPKPLDISEPEGKNYTITGNTLRWR 348 Query: 252 NWKFHVGFTARAGVTISTASVLDPRTKRFRRVMYRGHVSETFVPYMDPTYEWYYRTFMDI 311 NW+ H +R G+ ST + D KR ++MY G + VPY DP WY++ ++D Sbjct: 349 NWEMHFKLDSRVGLMFSTVTYNDHGKKR--QIMYEGSLGGMIVPYGDPDVGWYFKAYLDS 406 Query: 312 GEFGFGRSAVNLQPLIDCPQNAAFLDGHVAGPDGTAQKMTNVMCVFEKNGYGASFRHTEI 371 GE+G G ++ D P N LD +A G + + + VFE+ G F+H E Sbjct: 407 GEYGMGTLTSPIERGKDAPDNVVLLDATLADTSGKPRTIPRAIGVFERYA-GPEFKHQEY 465 Query: 372 NVPGQVITSGEAEISLVVRMVATLGNYDYIVDWEFKKNGAIRVGVDLTGVLEVKAT-SYT 430 P + E LV+R ++T+GNYDYI DW F +NG I + TG+ VK S T Sbjct: 466 GQPNLSVERRE----LVIRWISTVGNYDYIFDWVFAENGTIGINAGATGIEAVKGVKSST 521 Query: 431 SNDQIT--ENVYGTLVAKNTIAVNHDHYLTYYLDLDVDGNGNSLVKAKLKTVRVTEVNKT 488 D + YGTL+ N + H H + LDLDVDG NSL + V N Sbjct: 522 MRDASAAEDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGQNNSLTEVD----PVVLPNTP 577 Query: 489 SSRRKSYWTVVKETAKTEADGRVRLGSDPVELLIVNPNKKTKIGNTVGYRLIP-----EH 543 R S V+ TA+TE + + + LL NPNK K+GN V Y+LIP Sbjct: 578 GGPRSSTMQTVQRTAETEQQAAQKFDASTIRLLS-NPNKFNKVGNPVSYQLIPYAGGTHP 636 Query: 544 LQATSLLTDDDYPELRAGYTKYPVWVTAYDRSERWAGGFYSDRSRGDDGLAVWSSRNREI 603 + + + D++ R + +WVT YD +R+ G Y +RS D GL + N+ I Sbjct: 637 IAKGANFSPDEWLNKRLSFMDRQLWVTRYDPQQRFPEGKYPNRSHEDTGLGAFVKDNQSI 696 Query: 604 ENKDIVMWYNVGFHHIPYQEDFPVMPTLHGGFTLRPSNFFDNDPLIG 650 N+D V+W G H+ E++P+MPT L+P NFFD P +G Sbjct: 697 VNQDDVVWLTTGTTHVARAEEWPIMPTEWVHVLLKPWNFFDETPTLG 743 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: 1207 Number of extensions: 69 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: 748 Length adjustment: 39 Effective length of query: 611 Effective length of database: 709 Effective search space: 433199 Effective search space used: 433199 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