GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Burkholderia phytofirmans PsJN

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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