Alignments for a candidate for ydiJ in Desulfuromusa kysingii DSM 7343

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Desulfuromusa kysingii DSM 7343

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate WP_092345686.1 BLU87_RS05840 FAD-binding oxidoreductase

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



>NCBI__GCF_900107645.1:WP_092345686.1
          Length = 1019

 Score =  961 bits (2483), Expect = 0.0
 Identities = 506/1018 (49%), Positives = 665/1018 (65%), Gaps = 22/1018 (2%)

Query: 2    IAQLSTVAPSANYPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDAD 61
            + Q  T+ P   Y  FL+AL  +GF G+I   YA+R  +ATDNS+YQ LPQA VFP +  
Sbjct: 5    LTQQETIKPV--YRLFLKALVQAGFAGEIETTYASRLAVATDNSVYQWLPQAVVFPCNTT 62

Query: 62   DVARVATLMGEPRFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRV 121
            DVA +  L  +P++  V  + RGGGTGTNGQSL DGI+VD SRHM  IL++NVEERWVRV
Sbjct: 63   DVALLMRLSQDPQYCCVSFSARGGGTGTNGQSLNDGIIVDTSRHMTRILDLNVEERWVRV 122

Query: 122  QAGTVKDQLNAALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHS 181
            +AG VKDQLN  L+PHGLFF+PELSTSNRAT+GGM+NTDASGQGS  YGKT DHVLE+ +
Sbjct: 123  EAGLVKDQLNDFLRPHGLFFSPELSTSNRATIGGMVNTDASGQGSLVYGKTSDHVLEITA 182

Query: 182  VLLGGERLHSLPIDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGY 241
            VL  G  L    +  AAL+       R GE+YR            IE TFP+LNR LTGY
Sbjct: 183  VLEDGSVLDCHAVSGAALKAKRDLQDREGEIYRQVWSTSRELRSEIEETFPQLNRFLTGY 242

Query: 242  DLAHLRD-EQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDA 300
            DL  + D E    NL  +LCG+EG+LG V E  L++ PIP    LVNV+Y SF  ALR A
Sbjct: 243  DLKQVYDPETEGLNLARLLCGSEGTLGLVTEITLSLDPIPTCRNLVNVKYDSFEAALRTA 302

Query: 301  NALMAHKPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVN 360
              ++  + LS+ETVDSKVL LA +DIVWHSV +     P +  LG+N+VEF G +  ++ 
Sbjct: 303  PFMLQAEALSVETVDSKVLDLARQDIVWHSVRDLITDVPGKEVLGLNIVEFAGCDEVQIQ 362

Query: 361  AKVQAFIQHLQSDTSVER-----LGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQP 415
             +V+A    L  D  + R     +G+ +     +V  +Y MRK++VGLLGN  G+ +P  
Sbjct: 363  HRVKALCTQL--DDMITRGDRGVVGYQVCVDLSSVQAIYAMRKKAVGLLGNTSGKRKPVA 420

Query: 416  FVEDTAVPPEQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKP 475
            F EDTAVPPE LADYI +FRALLD   LAYGMFGHVD GVLHVRPALD+ DP    L++ 
Sbjct: 421  FTEDTAVPPEHLADYINEFRALLDANNLAYGMFGHVDCGVLHVRPALDLCDPDDEILLRN 480

Query: 476  ISDAVAALTKRYGGLLWGEHGKGLRSEYVPEYFGE-LYPALQRLKGAFDPHNQLNPGKIC 534
            ISD V  LT +YGGL+WGEHG+G RSEY PE+FG  L+  L+++KGAFDPHN+LNPGKIC
Sbjct: 481  ISDQVVTLTAKYGGLMWGEHGRGFRSEYGPEFFGPILFAELRKIKGAFDPHNRLNPGKIC 540

Query: 535  TPLGSAEGLTPVDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKA 594
            TPL S+  L  VD V  RG +DR I       F +A+ CNGNG C+NY+ +  MCPS+K 
Sbjct: 541  TPLDSSSSLVSVDAVK-RGSIDRQIPAATRDSFNAALDCNGNGLCFNYETSSPMCPSFKQ 599

Query: 595  TRERQHSPKGRASLMREWLRLQGEANIDVLA---AARNKVSWLKGLPARLRNNRARNQGQ 651
            T +R+HSPKGRA+LMREWLRL   A + VLA   A       LK    ++ N+  ++ G+
Sbjct: 600  TGDRRHSPKGRAALMREWLRLLEVAGVKVLAEEKAIEQGGISLKEHIHKVYNSLQKHNGR 659

Query: 652  EDFSHEVYDAMAGCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFT 711
             DFSHEV +AM GCLACK+C+ QCP+KV+VPDFR+RF++LY+ RY RP +DYL+  +E  
Sbjct: 660  YDFSHEVMEAMQGCLACKACSSQCPVKVDVPDFRARFMQLYYQRYLRPAQDYLVSLVENY 719

Query: 712  IPYLAHAPGLYNAVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRE 771
             P +A AP L+N  +  +W+ ++    VGMVD PL+S  N Q  L+           L  
Sbjct: 720  APLMAKAPALFNFFLKCRWIQKITEWTVGMVDVPLLSYPNLQKKLSGHVATRFEWEELER 779

Query: 772  LTPAQRERSIVLVQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGA 831
            L+P +R++ + +VQD FT Y++  +++  + L  +LG+   L P+  NGKP H++GFL +
Sbjct: 780  LSPEERKKYVFVVQDPFTSYYDAEVVADLVLLIEKLGYHPRLVPFVPNGKPKHIKGFLRS 839

Query: 832  FAKAAIRNATQLKALADCGVPLVGLDPAMTLVYRQEYQKVPGLEGCP-KVLLPQEWLMDV 890
            F K A+++A  L  +   G+P++G DPAM L YR EY +V         VLL QEWL+ +
Sbjct: 840  FKKTAVKSADFLNRVQKLGIPMIGPDPAMVLCYRDEYAQVLAENRTDFNVLLIQEWLLSI 899

Query: 891  LPEQAPAAPGS---FRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYG 947
            L +Q P+ P S   F L  HCTEKT +P++   W ++F   G  L   A GCCGM+GTYG
Sbjct: 900  L-DQVPSHPSSTQKFYLFGHCTEKTAIPSTHDDWSRIFHHFGASLEPLAVGCCGMAGTYG 958

Query: 948  HEARNQETSRTIFEQSWATKLDK--DGEPLATGYSCRSQVKRMTERKMRHPLEVVLQY 1003
            H A+N   SR I+  SW   L    + + L +GYSCRSQVKR+  +++ HPL+ +L +
Sbjct: 959  HAAKNLTDSRDIYAMSWQPALANLPEQQCLVSGYSCRSQVKRIDGKRLHHPLQALLGF 1016


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: 2441
Number of extensions: 110
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1006
Length of database: 1019
Length adjustment: 45
Effective length of query: 961
Effective length of database: 974
Effective search space:   936014
Effective search space used:   936014
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)
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