Alignments for a candidate for ydiJ in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Shewanella oneidensis MR-1

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate 201781 SO2643 oxidoreductase, FAD-binding, putative (NCBI ptt file)

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



>FitnessBrowser__MR1:201781
          Length = 1013

 Score =  877 bits (2267), Expect = 0.0
 Identities = 464/1001 (46%), Positives = 630/1001 (62%), Gaps = 18/1001 (1%)

Query: 14   YPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEP 73
            Y  +L+AL  S + G I   Y+ R V ATDNS+YQ LPQA ++P    D+     L  + 
Sbjct: 15   YLAYLDALEQSAYAGDIDKRYSARLVQATDNSVYQFLPQAVLYPKHQKDIEIALKLAAKA 74

Query: 74   RFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAA 133
             F  V  + RGGGTGTNGQSLT G+++D+SR+MN +LE+N E+ WVRV+AG +KD LN A
Sbjct: 75   EFVGVTFSARGGGTGTNGQSLTHGLILDVSRYMNRVLEVNPEQGWVRVEAGVIKDALNDA 134

Query: 134  LKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLP 193
            L+PHG FF+P+LSTSNRAT+GGMINTDASG GS  YGKT DHVL L SVL+ G  L + P
Sbjct: 135  LRPHGFFFSPDLSTSNRATIGGMINTDASGAGSLVYGKTSDHVLALRSVLIDGSVLDTRP 194

Query: 194  IDDAAL-EQACAAPGRVGE-VYRMAREIQETQAELIETTFPKLNRCLTGYDLAHLRDE-Q 250
            +D   L +    +   +G+ +     ++   + E IE  FPKLNR LTGYDL H+ +   
Sbjct: 195  LDAGVLGDPDNVSDNPLGQKLISSIAQVCRDKREQIEKQFPKLNRFLTGYDLKHVWNAGL 254

Query: 251  GRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLS 310
             +F+L+ +L G+EG+L  + EAKLN+ P+P    +VN++Y SF  ALR A +L+A +   
Sbjct: 255  TQFDLSRILTGSEGTLAVITEAKLNITPLPSERAMVNIKYDSFQSALRHAPSLVAARATV 314

Query: 311  IETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGD--EPAEVNAKVQAFIQ 368
            +ETVDSKVL LA +DIVWHSV++     P +   G+N+VEF GD  E  +  A ++A + 
Sbjct: 315  VETVDSKVLNLAREDIVWHSVSDLIQEVPGKTIDGLNMVEFAGDTAEVEQKLASLEAVLT 374

Query: 369  HLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLA 428
               S      +G+ + +   ++ ++Y MRK++VGLLG  +G  +P  F EDTAVPPE+LA
Sbjct: 375  EQISRGECGVVGYQVTQDKASIEKIYGMRKKAVGLLGATKGRRKPIAFAEDTAVPPEKLA 434

Query: 429  DYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYG 488
            DYI +FRALLD + L YGMFGHVDAGVLHVRPALDM D     L++ ISD VAALT +YG
Sbjct: 435  DYIMEFRALLDSHNLQYGMFGHVDAGVLHVRPALDMCDVEDEKLLRVISDQVAALTLKYG 494

Query: 489  GLLWGEHGKGLRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGLTPVD 547
            GL+WGEHGKG+R +Y P  FG ELY  LQ +KG FDP N+LNPGK+  P         VD
Sbjct: 495  GLMWGEHGKGVRGQYGPAVFGDELYGVLQEIKGLFDPDNRLNPGKLVAPKQVGSLAFDVD 554

Query: 548  GVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPKGRAS 607
              T RG  DR I   V   FP  ++CNGNG C+NY     MCPS+K T +R  SPKGRA 
Sbjct: 555  S-TKRGQFDRQIPVAVRDAFPDVMNCNGNGLCFNYSSYSPMCPSFKVTGDRVQSPKGRAG 613

Query: 608  LMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAGCLA 667
            LMREWLRL     +DV A A+ K     G+  R++N     +   D+SHEV +++ GCLA
Sbjct: 614  LMREWLRLLESEGVDVNALAKAKP---LGILQRMQNT-INAKRDYDYSHEVMESLKGCLA 669

Query: 668  CKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMG 727
            CK+C+ QCP+KV+VP FR++F  +Y+ RY RP +DYL+  +E ++P +A AP L N    
Sbjct: 670  CKACSSQCPVKVDVPKFRAQFFNIYYQRYLRPAKDYLVAGIEDSLPIMAAAPKLTNFASQ 729

Query: 728  SKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDA 787
            +     ++   +G VD+P +S    +  L         + AL+ +  A+R + +++VQD 
Sbjct: 730  NPLSQWVIKKAIGYVDAPALSVPTLKQRLDGHASRGYDLAALQAIPVAERSKFVLVVQDP 789

Query: 788  FTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLKALA 847
            F  +++  L+  FI L   LG +  L P+  NGKP H++GFL  FAK A  +A  L  + 
Sbjct: 790  FNSFYDAGLVYRFIQLIETLGLKPVLLPFKPNGKPTHIKGFLDKFAKTAQSSADFLNQVH 849

Query: 848  DCGVPLVGLDPAMTLVYRQEYQKVPGL-EGCPKVLLPQEWLMDVLPEQAPAAP---GSFR 903
              G+P++G+DPA+ L YR EY++V G   G  +V L  EWL+ +L    PA P     F 
Sbjct: 850  KLGMPMIGIDPALVLCYRDEYKEVLGANRGSFEVKLANEWLLGIL-HHIPAKPMQDKQFT 908

Query: 904  LMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIFEQS 963
              +HCTE T  P +  +W ++F+  G KL     GCCGM+GTYGHEA N E S+ +F+ S
Sbjct: 909  WFSHCTESTAKPNTANEWTKIFSHFGTKLTAVNLGCCGMAGTYGHEAENLERSKALFDMS 968

Query: 964  WATKLDK--DGEPLATGYSCRSQVKRMTERKMRHPLEVVLQ 1002
            W   L K    + L +GYSCRSQVKR    K +HPLE +L+
Sbjct: 969  WKNTLSKMDQSQVLVSGYSCRSQVKRFAGYKPKHPLEALLE 1009


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: 2363
Number of extensions: 91
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: 1013
Length adjustment: 45
Effective length of query: 961
Effective length of database: 968
Effective search space:   930248
Effective search space used:   930248
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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Candidates (tab-delimited)
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 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