Alignments for a candidate for ydiJ in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Halomonas desiderata SP1

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate WP_086511814.1 BZY95_RS20885 FAD-binding oxidoreductase

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



>NCBI__GCF_002151265.1:WP_086511814.1
          Length = 1002

 Score =  334 bits (857), Expect = 2e-95
 Identities = 309/1041 (29%), Positives = 461/1041 (44%), Gaps = 108/1041 (10%)

Query: 7   TVAPSANYPEFLE--ALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVA 64
           +VAP A      E  A  +    G++  D+A R   +TD SIYQ +P   V P    D+ 
Sbjct: 8   SVAPDARVKPVTELAARLSREMEGEVLFDHAARGRYSTDASIYQVMPLGVVIPRHQRDLT 67

Query: 65  RVATLMGEPRFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAG 124
              T++   R  QV +  RG GT   GQ++ + +V+D +R +  I+E + E   V V+ G
Sbjct: 68  ---TVLEAARDAQVPILARGAGTSQCGQTVGEALVIDTTRWLREIVEFDREAATVVVEPG 124

Query: 125 TVKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLL 184
            V D LNA LKPHGL++  ++STS + T+GGM   ++ G  S  YG    +VL + + L 
Sbjct: 125 IVLDHLNAWLKPHGLWYPVDVSTSAQCTLGGMAGNNSCGSRSIRYGNMVHNVLGIEAWLA 184

Query: 185 GGERLHSLPIDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDL- 243
            G   H    D+  L+      GR   +    + I E  +  I   FPK+ R + GY+L 
Sbjct: 185 DGSEAHFGFFDELPLK------GRERALAERVKAIAEGVSAEIREHFPKVLRRVGGYNLD 238

Query: 244 ------AHLRDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDAL 297
                     D QGR NL  +L GAEG+LG     KL + P+P + VL  V + +F  A+
Sbjct: 239 LFDCQNPKPYDPQGRVNLAHLLVGAEGTLGVSRRIKLRLSPLPTHKVLGVVNFPTFYQAM 298

Query: 298 RDANALMAHKPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPA 357
                ++   P ++E VD  ++ L++++  +  V E   A   RP   + LVEF G+E  
Sbjct: 299 DFTQHIVTLDPTAVELVDRTMIDLSLENPAFRPVIE--KALIGRPQ-AVLLVEFAGEERQ 355

Query: 358 EVNAKVQAFIQHLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFV 417
              A ++  +  L +D  +      + E A A   ++ +RK  + ++ +++G+ +P  F+
Sbjct: 356 TQLASLKR-LTELMADLGLPGSVVEMPEPA-AQAALWNVRKAGLNIMMSMKGDGKPVSFI 413

Query: 418 EDTAVPPEQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPIS 477
           ED AVP E LA+Y      +   +G     + H   G LHVRP LDM+    A  ++ I+
Sbjct: 414 EDCAVPLEHLAEYTDKLTEVFHRHGTEGTWYAHASVGTLHVRPILDMRRG-GARKMREIA 472

Query: 478 DAVAALTKRYGGLLWGEHGKGL-RSEYVPEYFGE-LYPALQRLKGAFDPHNQLNPGKIC- 534
           +  +AL ++Y G   GEHG GL R E+V   FGE L  A + +KGAFDP N LNPGKI  
Sbjct: 473 EEASALVRQYKGAYSGEHGDGLCRGEWVAWQFGETLNDAFRAIKGAFDPQNLLNPGKIVD 532

Query: 535 TPLGSAEGLTPVDGVTLRGDLDRTIDERVWQ--------------DFPSAVH-------- 572
           TP    E          R  L    D   W                   A H        
Sbjct: 533 TPKMDDERYFRFSTRYRRIPLTPLFDWSAWNVTRDPLTGELGEPGSAGDATHGLAMAVEM 592

Query: 573 CNGNGACYNYDPNDAMCPSWKATRERQHSPKGRASLMREWLRLQGEANIDVLAAARNKVS 632
           CN NG C  +D    MCPS++ TR+ QH  +GRA+ +R  L L G+              
Sbjct: 593 CNNNGHCRKFDAG-TMCPSYRITRDEQHLTRGRANTLR--LVLSGQLG------------ 637

Query: 633 WLKGLPARLRNNRARNQGQEDFSHEVYDAMAGCLACKSCAGQCPIKVNVPDFRSRFLELY 692
                           QG  D    V +A+  C++CK C   CP  V++  F+       
Sbjct: 638 ---------------EQGLAD--DAVKEALDLCVSCKGCKRDCPTGVDMAKFKIEARAAR 680

Query: 693 HGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMGSKWVSQLLADKVGMVDSPLISRFNF 752
                  LRD LIG +    P+     GL  AV    +++  L   +G        +  F
Sbjct: 681 VRTKGLALRDRLIGEMPRYAPWAKRFAGLLGAVERLDFLAHPLKRALGFA-----PQRRF 735

Query: 753 QATLTRCRVGMATVPALRELTPAQRERSIVLVQDAFTRYFETPLLSAFIDLAHRLGHRVF 812
            A            PAL   +  Q    +VL  D F  Y E+    A   +    G+RV 
Sbjct: 736 PAFTGDFLGEHHGTPAL--ASSVQPVGEVVLFVDTFNNYMESDNARAAKRVLEAAGYRVH 793

Query: 813 LAPYSANGKPLHVQGFL--GAFAKAAIRNATQLKAL---ADCGVPLVGLDPAMTLVYRQE 867
           L            + +L  G F KA       L AL    + GV +VGL+P+  L  R E
Sbjct: 794 LNVKPGERPLCCGRTYLSSGQFDKAKAEARRTLDALMPHVERGVAVVGLEPSCLLGMRDE 853

Query: 868 YQKVPGLEG----CPKVLLPQEWLMDV-----LPEQAPAAPGSFRLMAHCTEKTNVPAST 918
           + +    E         +L +E+L+       L       PG   L  HC +K     + 
Sbjct: 854 FLQYGFGEQARALADAAMLFEEFLVKARQAGELSLDLKPLPGRALLHGHCHQKAF--DAL 911

Query: 919 RQWEQVFARL-GLKLVTEATGCCGMSGTYGHEARNQETSRTIFEQSWATKL---DKDGEP 974
           R  EQV + +  L +    + CCGM+G++G+EA + + S  + E S    +   D D   
Sbjct: 912 RPVEQVLSWIPDLTVEIVDSSCCGMAGSFGYEAEHYDASLQMAELSLLPAIREADDDTVL 971

Query: 975 LATGYSCRSQVKRMTERKMRH 995
           +A G SCR Q++  + R+  H
Sbjct: 972 VADGTSCRHQIRDGSGREAIH 992


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: 2433
Number of extensions: 152
Number of successful extensions: 17
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 1006
Length of database: 1002
Length adjustment: 44
Effective length of query: 962
Effective length of database: 958
Effective search space:   921596
Effective search space used:   921596
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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