Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate 7024559 Shewana3_1737 FAD linked oxidase domain-containing protein (RefSeq)
Query= reanno::Putida:PP_4493 (1006 letters) >lcl|FitnessBrowser__ANA3:7024559 Shewana3_1737 FAD linked oxidase domain-containing protein (RefSeq) Length = 1013 Score = 873 bits (2255), Expect = 0.0 Identities = 462/1004 (46%), Positives = 628/1004 (62%), Gaps = 24/1004 (2%) Query: 14 YPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEP 73 Y +L+AL SG+ G I Y+ R V ATDNS+YQ LPQA ++P D+ +L + Sbjct: 15 YLAYLDALAQSGYAGDIDKRYSARLVQATDNSVYQFLPQAVLYPKHQKDIQIALSLAAKA 74 Query: 74 RFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAA 133 F V + RGGGTGTNGQSLT G+++D+SR+MN +LE+N E+ WVRV+AG VKD LN A Sbjct: 75 EFAGVTFSARGGGTGTNGQSLTHGLILDVSRYMNRVLEVNHEQGWVRVEAGVVKDALNDA 134 Query: 134 LKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLP 193 L+PHG FF+P+LSTSNRAT+GGMINTDASG GS YGKT DHVL L S+L+ G + P Sbjct: 135 LRPHGYFFSPDLSTSNRATIGGMINTDASGAGSLVYGKTSDHVLALRSILIDGSVFDTRP 194 Query: 194 IDDAALEQACAAPGRVGE------VYRMAREIQETQAELIETTFPKLNRCLTGYDLAHL- 246 +D L P V + + E+ + LIE FPKLNR LTGYDL ++ Sbjct: 195 LDAGLL----CNPDNVSDNPLGQKLISAIAEVCREKRALIEQQFPKLNRFLTGYDLKNVW 250 Query: 247 RDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAH 306 + +F+L+ +L G+EG+L + EAKLN+ P+P +VN++Y SF ALR A +L+A Sbjct: 251 NNGLTQFDLSRILTGSEGTLAVITEAKLNITPLPSERAMVNIKYDSFQSALRHAPSLVAA 310 Query: 307 KPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGD--EPAEVNAKVQ 364 + +ETVDSKVL LA +DIVWHSV++ P + G+N+VEF GD E +E A ++ Sbjct: 311 RATVVETVDSKVLNLAREDIVWHSVSDLIQEVPGKVIDGLNMVEFAGDAVEVSEKLAALE 370 Query: 365 AFIQHLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPP 424 A + + +G+ + + ++ ++Y MRK++VGLLG +G +P F EDTAVPP Sbjct: 371 AVLTEQINRGECGVVGYQVTQDKASIEKIYGMRKKAVGLLGATKGRRKPIAFAEDTAVPP 430 Query: 425 EQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALT 484 E LADYI +FRALLD + L YGMFGHVDAGVLHVRPALDM D L++ ISD VAALT Sbjct: 431 EMLADYIMEFRALLDSHNLQYGMFGHVDAGVLHVRPALDMCDVEDEKLLRVISDQVAALT 490 Query: 485 KRYGGLLWGEHGKGLRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGL 543 +YGGL+WGEHGKG+R EY P FG ELY LQ +KG FDP N+LNPGK+ P + Sbjct: 491 LKYGGLMWGEHGKGVRGEYGPSVFGDELYGVLQDIKGLFDPDNRLNPGKLVAPKQAGGLC 550 Query: 544 TPVDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPK 603 VD T RG DR I V +P ++CNGNG C+NY MCPS+K T +R SPK Sbjct: 551 FDVDS-TKRGKFDRQIPVEVRDAYPDVMNCNGNGLCFNYSSFSPMCPSFKVTGDRVQSPK 609 Query: 604 GRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYDAMA 663 GRA LMREWLRL +DV A AR K G+ R++N + D+SHEV +++ Sbjct: 610 GRAGLMREWLRLLESEGVDVNALARAKP---LGILQRMQNT-INAKRDYDYSHEVMESLK 665 Query: 664 GCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYN 723 GCLACK+C+ QCP+KV+VP FR++F +Y+ RY RP +DYL+ +E ++P +A AP L N Sbjct: 666 GCLACKACSSQCPVKVDVPKFRAQFFNIYYQRYLRPAKDYLVAGIEDSLPIMAAAPRLTN 725 Query: 724 AVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVL 783 + ++ +G VD+P +S + L + AL+ + +R + +++ Sbjct: 726 FASQNPLSQWVIKKAIGYVDAPALSVPTLKQRLDGHASRGYDLAALQAIPADERAKFVLV 785 Query: 784 VQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQL 843 VQD F +++ L+ F+ L LG + L P+ NGKP H++GFL FAK A +A L Sbjct: 786 VQDPFNSFYDAGLVYRFVQLIETLGLKPVLLPFKPNGKPTHIKGFLDKFAKTAQSSADFL 845 Query: 844 KALADCGVPLVGLDPAMTLVYRQEYQKVPGL-EGCPKVLLPQEWLMDVLPEQAPAA--PG 900 + G+P+VG+DPA+ L YR EY+++ G G +V L EWL+ +L + A Sbjct: 846 NQVHKLGMPMVGIDPALVLCYRDEYKEILGANRGAFEVKLANEWLLSILQDIPTKAMQDK 905 Query: 901 SFRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIF 960 F +HCTE T P + +W ++F G KL GCCGM+GTYGHEA N E S+T+F Sbjct: 906 QFTWFSHCTESTAKPNTANEWSKIFTHFGAKLTAVNLGCCGMAGTYGHEAENLERSKTLF 965 Query: 961 EQSWATKLDK--DGEPLATGYSCRSQVKRMTERKMRHPLEVVLQ 1002 + SW L + + L +GYSCRSQVKR K +HPLE +L+ Sbjct: 966 DMSWKDTLSRIDASQVLVSGYSCRSQVKRFAGYKPKHPLEALLE 1009 Lambda K H 0.320 0.135 0.409 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: 2373 Number of extensions: 90 Number of successful extensions: 10 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: 1006 Length of database: 1013 Length adjustment: 45 Effective length of query: 961 Effective length of database: 968 Effective search space: 930248 Effective search space used: 930248 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: 57 (26.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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