Alignments for a candidate for ydiJ in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Dinoroseobacter shibae DFL-12

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate 3609942 Dshi_3324 FAD linked oxidase domain protein (RefSeq)

Query= reanno::Putida:PP_4493
         (1006 letters)



>FitnessBrowser__Dino:3609942
          Length = 973

 Score =  338 bits (866), Expect = 1e-96
 Identities = 295/1010 (29%), Positives = 458/1010 (45%), Gaps = 103/1010 (10%)

Query: 28   GQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEPRFQQVKLTPRGGGT 87
            G++  D  +R   ATD SIYQ  P  AV P   DD+    T +G  R     + PRGGGT
Sbjct: 19   GELLFDAFSRGRYATDASIYQMTPLGAVVPKSLDDIE---TALGAARELGASVLPRGGGT 75

Query: 88   GTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAALKPHGLFFAPELST 147
               GQ++   +V+D S++ N IL+++V  R   VQ G V D+LN ALKPHGL+F  ++ST
Sbjct: 76   SQCGQTVNHSLVLDNSKYFNRILDLDVANRRCVVQPGIVLDELNRALKPHGLWFPVDVST 135

Query: 148  SNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLPIDDAALEQACAAPG 207
            ++RAT+GGM   ++ G  S  YG  RD+VL + ++L  G R    P+D   +        
Sbjct: 136  ASRATIGGMAANNSCGGRSLRYGTMRDNVLSIEAILADGTRTTFGPVDRNGVLGNDPTSA 195

Query: 208  RVGEVYRM-AREIQETQAELIETTFPKLNRCLTGYDLAHLRDEQGRFNLNSVLCGAEGSL 266
             + E+  + ARE    QAE I   FP + R + GY++  L  +  R N+  +L G+EG+L
Sbjct: 196  LISEMLALGARE----QAE-IAARFPNIIRRVGGYNIDALTPDHARNNMAHLLVGSEGTL 250

Query: 267  GYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLSIETVDSKVLMLAMKDI 326
            GY    +L + P+    V     + +F  A+  A  L+  KP ++E VD  ++ LA +DI
Sbjct: 251  GYFTAIELKLSPLQSTKVTGACHFPTFHAAMDAAQHLVPLKPAAVELVDDTMIALA-RDI 309

Query: 327  VW--HSVAEYFPADPERPTLGINLVEFCGDEPAEVNAKVQAFIQHLQS-----DTSVERL 379
                 +++++   DP      + LVEF     A   AK++     + +     D S +  
Sbjct: 310  PMFRQTISQFVQGDP----AALLLVEFAEGSDAANAAKLEELSDKMAALGFGFDRSGKHW 365

Query: 380  GHTLA-EGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLADYIADFRALL 438
            G ++A    +    +  +RK  + ++ +++ E +P  FVED AV    LA Y A    + 
Sbjct: 366  GGSVAVTDLKLQNDIGEVRKSGLNIMMSMKSEGKPVSFVEDCAVELPDLAAYTAGLTEIF 425

Query: 439  DGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGGLLWGEHGKG 498
            + +G     + H   G LHVRP L+MK       ++ I++    L   Y G   GEHG G
Sbjct: 426  EKHGTKGTWYAHASVGCLHVRPVLNMKLDKDVKTMRAIAEECFDLVAHYKGSHSGEHGDG 485

Query: 499  L-RSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTP--LGSAEGLTPVDGVTLRGD 554
            + RSE+  + FG ++  +   +K  FDP+   NPGKI  P  +            T++  
Sbjct: 486  IVRSEFHEKMFGPQMVASFNEVKDRFDPNRLFNPGKIVQPPKMDDRRLFRYGPDYTVK-P 544

Query: 555  LDRTIDERVWQ----DFPSAVH-CNGNGACYNYDPNDAMCPSWKATRERQHSPKGRASLM 609
            +   +D   W      F  AV  CN NGAC        MCPS++ TR  +   +GRA+ +
Sbjct: 545  MKTALDWSAWPGAGGGFQGAVEMCNNNGACRKL-KGGVMCPSYRVTRNERDVVRGRANSL 603

Query: 610  REWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAGCLACK 669
            R  L + G+   D  A                             S ++  AM  C++CK
Sbjct: 604  R--LAISGQLGPDAFA-----------------------------SDDMVSAMKLCVSCK 632

Query: 670  SCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMGSK 729
             C  +CP  V++   +   L     ++     D L+G +    P+ A  P L NA     
Sbjct: 633  GCKRECPTGVDMAKMKIEVLAARAEKHGLSFHDKLVGYMPAYAPFAAKLPWLANARNWLP 692

Query: 730  WVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDAFT 789
              ++L     G   S  +  ++    L              +      +  +VL  D F 
Sbjct: 693  GAAKLTERLTGFAASRKLPAWSNDPFL--------------DTEFQDADPDVVLWADIFN 738

Query: 790  RYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPL-----HVQGFLGAFAKAAIRNATQLK 844
            RYFE   L A   +    G RV +   +    PL     ++   L   A+A+ R A  LK
Sbjct: 739  RYFEPENLRAAGRVLRAAGLRVAVVRPADGKDPLDCGRTYLAVGLVEEARASARRA--LK 796

Query: 845  AL---ADCGVPLVGLDPAMTLVYRQEYQ-KVPGLEG---CPKVLLPQEWLMD---VLPEQ 894
            AL   A+ GVP+VGL+P+  L  R E+   VPG E        L+ +E+L+     LP +
Sbjct: 797  ALVPHAEKGVPIVGLEPSSLLTLRDEWPVLVPGPEADLVAQHALMLEEYLVRNEIALPLK 856

Query: 895  APAAPGSFRLMAHCTEKT-NVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQ 953
                P    L  HC +K  NV    ++   +  +  + +V   T CCGM+G +G+     
Sbjct: 857  PLGRP--ILLHGHCHQKAHNVMPDVQKTLAMIPQAEVSVV--ETSCCGMAGAFGYGKDTV 912

Query: 954  ETSRTIFEQSWATKL---DKDGEPLATGYSCRSQVKRMTERKMRHPLEVV 1000
            ETS  + E      +    +D   +A G SCR Q+K    R+  H   ++
Sbjct: 913  ETSLKMAELDLLPAVRAAAQDALVVADGTSCRHQIKDGAAREAIHVARIL 962


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: 2214
Number of extensions: 121
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 1006
Length of database: 973
Length adjustment: 44
Effective length of query: 962
Effective length of database: 929
Effective search space:   893698
Effective search space used:   893698
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources