Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate 6937930 Sama_2071 oxidoreductase, FAD-binding, putative (RefSeq)
Query= reanno::Putida:PP_4493 (1006 letters) >FitnessBrowser__SB2B:6937930 Length = 1007 Score = 899 bits (2323), Expect = 0.0 Identities = 475/1001 (47%), Positives = 646/1001 (64%), Gaps = 22/1001 (2%) Query: 14 YPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEP 73 Y FLEAL + F G+I Y+ R V ATDNS+YQ LPQA ++P DV RV L + Sbjct: 15 YLAFLEALA-ADFDGEIDTRYSARIVQATDNSVYQFLPQAVLYPKSTLDVQRVMQLAAKD 73 Query: 74 RFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAA 133 F++V + RGGGTGTNGQSLT G+++DLSRHMN +LE+N EE W RV+AG VKD LN A Sbjct: 74 EFREVVFSARGGGTGTNGQSLTHGLILDLSRHMNKVLEVNAEEGWARVEAGVVKDALNDA 133 Query: 134 LKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLP 193 L+PHG FF+P+LSTSNRAT+GGMINTDASG GS YGKT DHVL L SVL+ G L S+P Sbjct: 134 LRPHGFFFSPDLSTSNRATLGGMINTDASGAGSLVYGKTSDHVLGLKSVLIDGSVLDSVP 193 Query: 194 IDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDLAHLRDEQ-GR 252 + +L+ + G++ + + EL++T FP+LNR LTGYDL H+ D+ + Sbjct: 194 MAAESLD-TVDSRSLAGKLIANISAVCRDKRELVKTRFPRLNRFLTGYDLEHVWDDDLSQ 252 Query: 253 FNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLSIE 312 F+L+ +L G+EG+L + EAK+N+ P+PK +VN++Y SF ALR A +L+A +E Sbjct: 253 FDLSRILTGSEGTLAVITEAKVNLTPLPKQRAMVNIKYDSFESALRHAPSLVAASATVVE 312 Query: 313 TVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAK---VQAFIQH 369 TVDSKVL LA +DIVWHSV+E P + G+N+VEF GDE AEVNAK ++A + Sbjct: 313 TVDSKVLGLAREDIVWHSVSELIQEVPGKHIDGLNMVEFAGDE-AEVNAKLAALEAVLAE 371 Query: 370 LQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLAD 429 + +G ++ ++Y MRK++VGLLG +G +P F EDTAVPPE+LAD Sbjct: 372 QIKNGECGVVGFRSTHDKVSIEKIYAMRKKAVGLLGAAKGSRKPIAFAEDTAVPPEKLAD 431 Query: 430 YIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGG 489 +I +FRALLDG+ L YGMFGHVDAGVLHVRPALDM DPV L++ ISD VAALT +YGG Sbjct: 432 FIMEFRALLDGHKLQYGMFGHVDAGVLHVRPALDMCDPVDEKLLRTISDEVAALTLKYGG 491 Query: 490 LLWGEHGKGLRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGLTPVDG 548 L+WGEHGKG+R EY P FG ELY LQ +KG FDP N+LNPGK+ P E VD Sbjct: 492 LMWGEHGKGVRGEYGPAVFGDELYGVLQDIKGWFDPDNRLNPGKLVAPKDKGELFYNVDS 551 Query: 549 VTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPKGRASL 608 RG DR I +V + FP ++CNGNG C+NY MCPS+K T +R SPKGR+SL Sbjct: 552 AK-RGSFDRQIPVKVREAFPDVMNCNGNGLCFNYSAYSPMCPSFKVTGDRIQSPKGRSSL 610 Query: 609 MREWLRLQGEANIDVLAAARNK-VSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAGCLA 667 MREWLRL +DV A++K + WL + N + + + D+SHEV +++ GCLA Sbjct: 611 MREWLRLLEAEGVDVEQLAKSKPLGWL-----QRAQNSLKAKDEYDYSHEVMESLKGCLA 665 Query: 668 CKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMG 727 CK+C+GQCP+KV+VP FR++F +Y+ RY RP +DYL+ +E +P +A AP L NA+ Sbjct: 666 CKACSGQCPVKVDVPKFRAQFFNIYYQRYLRPPKDYLVAGIEDALPLMAKAPKLVNALSQ 725 Query: 728 SKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDA 787 + ++ +G VD+P +S L + + +L+ + A+R R +++ QD Sbjct: 726 NSLSQWVIKKAIGYVDAPKLSVPTLTQRLESHQSLGYDLESLKRIPAAERSRYVLVAQDP 785 Query: 788 FTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLKALA 847 F +++ L+ F+ L +LG + L P+ NGKP H++GFL FA +A A L Sbjct: 786 FNSFYDAGLVYHFVKLIEKLGFKPVLLPFKPNGKPAHIKGFLDKFAASAGTAAAFFNELG 845 Query: 848 DCGVPLVGLDPAMTLVYRQEYQKVPGLE-GCPKVLLPQEWLMDV---LPEQAPAAPGSFR 903 G+P+VG+DPAM LVYR EY+ G + G + L EWLM+V LP++ + G + Sbjct: 846 KLGMPMVGVDPAMVLVYRDEYKVALGKDRGDFNIKLANEWLMEVLEALPQRELSGRG-YT 904 Query: 904 LMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIFEQS 963 +HCTE T P + ++W +FAR G L + GCCGM+GTYGHE N S+ +++ S Sbjct: 905 WFSHCTESTAKPGTAKEWSAIFARFGATLKVKNLGCCGMAGTYGHELDNLARSQQLYDMS 964 Query: 964 WATKLDKDG--EPLATGYSCRSQVKRMTERKMRHPLEVVLQ 1002 W ++ E L +GYSCRSQVKR + + +HPLE +L+ Sbjct: 965 WKEGINGTSREEILVSGYSCRSQVKRFSGFRPKHPLEALLE 1005 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: 2367 Number of extensions: 110 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: 1007 Length adjustment: 45 Effective length of query: 961 Effective length of database: 962 Effective search space: 924482 Effective search space used: 924482 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