Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS33430 BPHYT_RS33430 dimethylmenaquinone methyltransferase
Query= reanno::Putida:PP_4493 (1006 letters) >FitnessBrowser__BFirm:BPHYT_RS33430 Length = 999 Score = 376 bits (966), Expect = e-108 Identities = 296/1008 (29%), Positives = 460/1008 (45%), Gaps = 76/1008 (7%) Query: 18 LEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEPRFQQ 77 LEA S RG++ D ++ + A D S Y+++P A V P D DD+ +ATL R Sbjct: 44 LEADLRSHVRGEVRFDQGSKALYAADASNYRQVPLAVVVPADVDDL--LATLAACRR-ND 100 Query: 78 VKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAALKPH 137 V PRGGGT NGQ + +V D S+++N ++ ++ R V+ G V D L A + H Sbjct: 101 VPFLPRGGGTSQNGQCVNVAVVADASKYVNRVVSVDPVARVAIVEPGVVCDTLRDAAEQH 160 Query: 138 GLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLPIDDA 197 GL FAP+ +T +R T+GGMI ++ G S GKT ++V L G R P D Sbjct: 161 GLTFAPDPATHSRCTLGGMIANNSCGAHSVMAGKTVENVEALEIATFDGARFWVGPTSDQ 220 Query: 198 ALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDLAHLRDEQGRFNLNS 257 LE AA GR GE+Y +++++T AE I FP++ R ++G++L L E G FN+ Sbjct: 221 ELEHIIAAGGRQGEIYAALKQLRDTYAEQIRARFPQIKRRVSGFNLDQLLPENG-FNVAR 279 Query: 258 VLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLSIETVDSK 317 L G EG+ ++AK+ ++ P V+V V +T A M +P+++E +D Sbjct: 280 ALVGTEGTCALTLQAKVRLVKSPAMRVIVVVGFTDIYTAADAVPHFMRCEPIAVEGLDRA 339 Query: 318 VLM-LAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAKVQAFIQHLQSDTSV 376 ++ L + + +A D ++EF D +V K +A S + Sbjct: 340 IIRGLQARGLKKDEIALLPEGD------AWVVLEFGADTQDDVMLKARAAAACFASGEAG 393 Query: 377 ERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFV--EDTAVPPEQLADYIADF 434 + L E +V+++R+ + P P V ED AV P +L DY+ F Sbjct: 394 PNVSAMLVEDRALQAKVWSIRETGASAVALSVDSGTPDPVVGWEDAAVDPLRLGDYLRAF 453 Query: 435 RALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGGLLWGE 494 +AL+D YG ++GH G +H R D++ A + A L +GG L GE Sbjct: 454 QALVDRYGYETSLYGHFGDGCVHARITFDLRSAEGVATWRKFLREAAELVVEFGGSLSGE 513 Query: 495 HGKG-LRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGL---TPVDGV 549 HG G ++E++P +G EL A+++ K +DP N+LNPGK+ + E L V Sbjct: 514 HGDGQAKAEFLPIMYGPELMQAMEQFKAIWDPANRLNPGKVVHAYRADENLRMGPAYKPV 573 Query: 550 TLRGDLDRTIDERVWQDFPSAV-HCNGNGACYNYDPNDAMCPSWKATRERQHSPKGRASL 608 TL+ L T + + F + C G G C + + MCPS++ATRE ++S +GRA L Sbjct: 574 TLQTRL--TFASQEGEGFQREIERCIGMGKCRSLE-GGTMCPSYRATREEKYSTRGRAHL 630 Query: 609 MREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAGCLAC 668 W LQG+ D W S EV +A+ CLAC Sbjct: 631 F--WEMLQGDVIAD---------GWQ--------------------SREVKEALDTCLAC 659 Query: 669 KSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMGS 728 K C CP ++ +++ FL Y+ +RP + +G + P+ A P L N + + Sbjct: 660 KGCKSDCPTHTDMASYKAEFLSHYYETNRRPRQALFMGRIGEWAPWAARFPRLTNFMTSA 719 Query: 729 KWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDAF 788 +S G+ + + RF A T ++ + + R+ ++ ++L D F Sbjct: 720 PCLSSFGKWLAGVAQTRELPRF---ADATYRQIARRSPQSARDARGDVKK--VILWVDTF 774 Query: 789 TRYFETPLLSAFIDLAHRLGHRVFLAPYS-ANGKPLHVQGFLGAFAKAAIRNATQLKALA 847 +F + A D+ +LG V L G+PL+ G L + L Sbjct: 775 NDHFTPEIAQAAADVLKQLGWHVVLPKNRLCCGRPLYDFGLLERARELLTHILDDLADDI 834 Query: 848 DCGVPLVGLDPAMTLVYRQEYQKVPGLEGCPKVLLPQEWLM-DVLPEQA---PAAPGSFR 903 GVPLVGL+P V++ E K K L Q +L D + Q+ P Sbjct: 835 AAGVPLVGLEPGCLSVFKDELLKQLPNHALAKKLSAQTFLFSDFVARQSFDWPTLAADVI 894 Query: 904 LMAHCTEKT--NVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIFE 961 + HC +K + T + +LG+K TGCCGM+G++G A + S I E Sbjct: 895 VHGHCHQKALFGMQGDT----ALLNKLGVKWKLLDTGCCGMAGSFGFNAEHHALSTKIGE 950 Query: 962 QSW---ATKLDKDGEPLATGYSCRSQVKRMTERKMRHPLEVVLQYAQR 1006 + L G+SCR Q+++ T R H + Q AQR Sbjct: 951 DKLFPAVRAASVETIVLTNGFSCREQIEQGTGRHAMH----IAQLAQR 994 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: 2158 Number of extensions: 80 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 1006 Length of database: 999 Length adjustment: 44 Effective length of query: 962 Effective length of database: 955 Effective search space: 918710 Effective search space used: 918710 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