Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate BWI76_RS17050 BWI76_RS17050 FAD-binding oxidoreductase
Query= reanno::Putida:PP_4493 (1006 letters) >FitnessBrowser__Koxy:BWI76_RS17050 Length = 1018 Score = 992 bits (2565), Expect = 0.0 Identities = 508/999 (50%), Positives = 668/999 (66%), Gaps = 14/999 (1%) Query: 17 FLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEPRFQ 76 FL+ L GF G + YA R +ATDNS+YQ LP A +FP DVA +A L E RF+ Sbjct: 18 FLQVLEQQGFTGDTATSYADRLTMATDNSVYQLLPDAIIFPRSTADVALLARLAAEERFK 77 Query: 77 QVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAALKP 136 + TPRGGGTGTNGQ+L GI+VD+SR+MN I+EIN EE WVRV+AG +KDQLN LKP Sbjct: 78 SLIFTPRGGGTGTNGQALNAGIIVDMSRYMNRIIEINPEEGWVRVEAGVIKDQLNQFLKP 137 Query: 137 HGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLPIDD 196 +G FFAPELSTSNRAT+GGMINTDASGQGS YGKT DHVL + SVL+GG+ L + PI Sbjct: 138 YGYFFAPELSTSNRATLGGMINTDASGQGSLVYGKTSDHVLGVRSVLIGGDILDTQPIPV 197 Query: 197 AALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDLAHL-RDEQGRFNL 255 A E A +G +YR + + Q +L+ FPKLNR LTGYDL H+ DE F+L Sbjct: 198 ALAETLSAQQSAIGRIYRTVYQRCKAQRQLVIDKFPKLNRFLTGYDLRHVFNDEMSEFDL 257 Query: 256 NSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLSIETVD 315 +L G+EG+L ++ EA+L++ +PK LVNV+Y SF ALR+A ++ + LS+ETVD Sbjct: 258 TRILTGSEGTLAFITEARLDITRLPKVRRLVNVKYDSFNSALRNAPFMVEARALSVETVD 317 Query: 316 SKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAKVQAFIQHLQ---S 372 SKVL LA +DIVWHSV+E ++ LG+N+VEF GD+ ++++V A Q L S Sbjct: 318 SKVLNLAREDIVWHSVSELITDVADKEMLGLNIVEFAGDDVELIDSQVTALCQRLDELIS 377 Query: 373 DTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLADYIA 432 +G + + V R+Y MRK++VGLLGN +G +P PF EDT VPPE LADYIA Sbjct: 378 RNEAGVIGWQVCHDLDGVERIYAMRKKAVGLLGNAKGAAKPIPFAEDTCVPPEHLADYIA 437 Query: 433 DFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGGLLW 492 +FRALLDG+GL+YGMFGHVDAGVLHVRPALDM DP Q L+K ISD V ALT +YGGLLW Sbjct: 438 EFRALLDGHGLSYGMFGHVDAGVLHVRPALDMCDPQQEMLMKRISDDVVALTAKYGGLLW 497 Query: 493 GEHGKGLRSEYVPEYFGE-LYPALQRLKGAFDPHNQLNPGKICTPLGSAEGLTPVDGVTL 551 GEHGKG R+EY P +FGE L+ L+++K AFDP N+LNPGKIC P G + VD V Sbjct: 498 GEHGKGFRAEYSPAFFGEALFGELRKIKAAFDPDNRLNPGKICPPEGVDAPMMKVDAVK- 556 Query: 552 RGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPKGRASLMRE 611 RG DR I V + A+ CNGNG C+N+D MCPS K + R HSPKGRA+L+RE Sbjct: 557 RGTFDRQIPIAVRSSWRGAMECNGNGLCFNFDAKSPMCPSMKVSNHRIHSPKGRATLVRE 616 Query: 612 WLRLQGEANIDVLAAARN---KVSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAGCLAC 668 WLRL + ID ++ K + L+ L R RN+ +G+ DFSHEV +AM+GCLAC Sbjct: 617 WLRLLADRGIDPNQLEKDLPEKRASLRTLVERTRNSWHARKGEYDFSHEVKEAMSGCLAC 676 Query: 669 KSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMGS 728 K+C+ QCPIK++VP+FRSRFL+LYH RY RP+RD+L+ ++E P +AHAP +N + Sbjct: 677 KACSTQCPIKIDVPEFRSRFLQLYHSRYLRPVRDHLVATVESYAPLMAHAPKTFNFFINQ 736 Query: 729 KWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDAF 788 W+ +L +GMVD PL+S + + + R T+ L EL+ Q+ + +++VQD F Sbjct: 737 PWMRKLSEKHIGMVDLPLLSVPSLKQQMVGHRSANTTLEQLEELSAEQKAKMVLVVQDPF 796 Query: 789 TRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLKALAD 848 T Y++ +++ F+ L ++G++ L P+S NGK H++GFL FA+ A + A L +A+ Sbjct: 797 TSYYDAQVVADFVRLVEKVGYQPVLLPFSPNGKAQHIKGFLTRFARTAQKTADFLNRVAE 856 Query: 849 CGVPLVGLDPAMTLVYRQEYQKVPG-LEGCPKVLLPQEWLMDVLPEQAPAAPG--SFRLM 905 G+P+VG+DPA+ L YR EY +V G G +V+L EWL L E A G S+ L Sbjct: 857 LGMPMVGVDPALVLCYRDEYNQVLGDKRGDFRVMLVHEWLPQALSETAAQDKGGESWYLF 916 Query: 906 AHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIFEQSWA 965 HCTE T +PASTRQW +FAR G KL + GCCGM+GTYGHE +N S I+ SW Sbjct: 917 GHCTEVTALPASTRQWADIFARFGAKLENVSVGCCGMAGTYGHEVKNHANSLAIYALSWQ 976 Query: 966 TKLDK--DGEPLATGYSCRSQVKRMTERKMRHPLEVVLQ 1002 +++ L TGYSCRSQVKR+ +RHPL+ +L+ Sbjct: 977 QAMERLPRNRCLVTGYSCRSQVKRIEGSGVRHPLQALLE 1015 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: 2385 Number of extensions: 91 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: 1006 Length of database: 1018 Length adjustment: 45 Effective length of query: 961 Effective length of database: 973 Effective search space: 935053 Effective search space used: 935053 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:
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