Alignments for a candidate for ydiJ in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Lacinutrix algicola AKS293

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate WP_055437104.1 ASC41_RS13085 FAD-binding oxidoreductase

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



>NCBI__GCF_001418085.1:WP_055437104.1
          Length = 970

 Score =  377 bits (969), Expect = e-108
 Identities = 281/1003 (28%), Positives = 462/1003 (46%), Gaps = 86/1003 (8%)

Query: 28   GQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEPRFQQVKLTPRGGGT 87
            G++      + + ATD S+Y+ LP A  FP    D+ ++     +    +  + PR  GT
Sbjct: 19   GELHYSDLMKRLYATDASVYRMLPLAVAFPKSNSDIKKLVVFATK---NKTSIIPRTAGT 75

Query: 88   GTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAALKPHGLFFAPELST 147
               GQ +  GIVVD+S++   IL IN   + V VQ G V+D+LN  LKP GLFF P  ST
Sbjct: 76   SLAGQCVGTGIVVDVSKYFTKILNINETNQTVTVQPGVVRDELNNHLKPFGLFFGPNTST 135

Query: 148  SNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLPIDDAALEQACAAPG 207
            SNR  +GGM+  ++SG  S  YG TRD VLEL ++L  G       +   AL+    +  
Sbjct: 136  SNRCMIGGMVGNNSSGTTSIRYGVTRDKVLELKTILSDGSEAVFSELTQEALQNKTKSNT 195

Query: 208  RVGEVY-RMAREI--QETQAELIETTFPK--LNRCLTGYDLAHLRDEQGRFNLNSVLCGA 262
              G++Y  +  E+  +ET+ E+I   FPK  ++R  TGY +  L +    FNL  +L G+
Sbjct: 196  LEGKIYSTVVSELSSEETRNEII-NNFPKPEIHRRNTGYAIDELINTTEAFNLCKLLSGS 254

Query: 263  EGSLGYVVEAKLNVLPIP-KYAVLVNVRYTSFMDALRDANALMAHKPLSIETVDSKVLML 321
            EG+L +  E  L +  +P   ++++   + +    L     +M H   + E +D  +L  
Sbjct: 255  EGTLAFTTEITLKLDKLPASQSIMIAAHFNTINACLEAVEPVMQHNLFTCEMMDKTILDC 314

Query: 322  AMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAKVQAFIQHLQSDTSVERLGH 381
               +       ++   DP+     I + E  G+    V  +    I+ L+ +T +     
Sbjct: 315  TKNNKTQTENRQFIQGDPQ----AILMCEVKGETLENVQIQANNLIETLE-NTGLSYANI 369

Query: 382  TLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLADYIADFRALLDGY 441
            +L    + + +   +RK  +GLLGN+ G+ +    +EDTAV    LA+YI++F AL+ G+
Sbjct: 370  SLVN--KEIDKANELRKAGLGLLGNIIGDKKAVACIEDTAVALPDLANYISEFTALMKGH 427

Query: 442  GLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGGLLWGEHGKGL-R 500
                  + H  AG +H+RP L++K      L + I+  VA L K+Y G   GEHG G+ R
Sbjct: 428  KQGAVYYAHAGAGEIHLRPILNLKKDEDVILFRKITTDVATLVKKYNGSFSGEHGDGIVR 487

Query: 501  SEYVPEYFGEL-YPALQRLKGAFDPHNQLNPGKICTPLGSAEGLT-PVDGVTLRGD--LD 556
            +E++    G+  Y  L+R+K  FDP N  NPGKI       + L   VD V  + +  LD
Sbjct: 488  AEFIKFMIGDKNYQLLKRIKSVFDPENIFNPGKIVEAFPMDKNLRYQVDRVEPKIETLLD 547

Query: 557  RTIDERVWQDFPSAVHCNGNGACYNY-DPNDAMCPSWKATRERQHSPKGRASLMREWLRL 615
             +  + + ++   A  CNG+G C    +    MCPS++ATR+ + + + RA+ +RE+L  
Sbjct: 548  FSASQGILRE---AEKCNGSGDCRKLPEFGGTMCPSYRATRDEKDTTRARANALREYLTN 604

Query: 616  QGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHE----VYDAMAGCLACKSC 671
              +AN                                 F HE    V+D    CL+CK+C
Sbjct: 605  SDKAN--------------------------------KFDHEELKQVFDL---CLSCKAC 629

Query: 672  AGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMGSKWV 731
            + +CP  V+V   ++ F   Y       LR  L           +  P L N +  + + 
Sbjct: 630  SSECPSSVDVATLKAEFQYQYQKVNGTNLRTKLFAYNNKLNAIGSKLPSLTNFMFSNGFT 689

Query: 732  SQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDAFTRY 791
            S +L   +G+     +   + ++     ++         E+   +  ++I L  D FT Y
Sbjct: 690  SSILKKTIGVATERSLPLISSKSLYKEYQI------IKNEIIKNKYIKTIYLFNDEFTNY 743

Query: 792  FETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLKALADCGV 851
             +T +    + L   L + V L   S +G+    +G L    K A RN    K +     
Sbjct: 744  LDTSIGVDAVTLLQALNYEVKLINNSESGRSFMSKGLLDEAKKVANRNIEIYKNVISEET 803

Query: 852  PLVGLDPAMTLVYRQEYQKVPGLEGCPKVLLPQEWLMD-----------VLPEQAPAAPG 900
            PLVG++P+  L +R EY K+   +   K +    +L++           + P Q  +   
Sbjct: 804  PLVGIEPSAILSFRGEYLKLVDDKVSAKAIAKNTFLIEEFLSNEIAIGNIKPSQFTSEEK 863

Query: 901  SFRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIF 960
            + +   HC +K         +  +      K+    +GCCGM+G++G+E  + + S  I 
Sbjct: 864  TIKFHGHCHQKAE-SNQIHSFNVLNLPKNYKVTIIPSGCCGMAGSFGYEKEHYKVSMQIG 922

Query: 961  EQSW---ATKLDKDGEPLATGYSCRSQVKRMTERKMRHPLEVV 1000
            EQ+          +    A G SCR Q+K  T+R   HP+ ++
Sbjct: 923  EQTLFPAVRNASLETTIAANGTSCRHQIKDGTQRTALHPITIL 965


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: 1874
Number of extensions: 77
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: 970
Length adjustment: 44
Effective length of query: 962
Effective length of database: 926
Effective search space:   890812
Effective search space used:   890812
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 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
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 2024 update 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