Alignments for a candidate for ydiJ in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Shewanella sp. ANA-3

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate 7024559 Shewana3_1737 FAD linked oxidase domain-containing protein (RefSeq)

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



>FitnessBrowser__ANA3:7024559
          Length = 1013

 Score =  873 bits (2255), Expect = 0.0
 Identities = 462/1004 (46%), Positives = 628/1004 (62%), Gaps = 24/1004 (2%)

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

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

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

Query: 194  IDDAALEQACAAPGRVGE------VYRMAREIQETQAELIETTFPKLNRCLTGYDLAHL- 246
            +D   L      P  V +      +     E+   +  LIE  FPKLNR LTGYDL ++ 
Sbjct: 195  LDAGLL----CNPDNVSDNPLGQKLISAIAEVCREKRALIEQQFPKLNRFLTGYDLKNVW 250

Query: 247  RDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAH 306
             +   +F+L+ +L G+EG+L  + EAKLN+ P+P    +VN++Y SF  ALR A +L+A 
Sbjct: 251  NNGLTQFDLSRILTGSEGTLAVITEAKLNITPLPSERAMVNIKYDSFQSALRHAPSLVAA 310

Query: 307  KPLSIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGD--EPAEVNAKVQ 364
            +   +ETVDSKVL LA +DIVWHSV++     P +   G+N+VEF GD  E +E  A ++
Sbjct: 311  RATVVETVDSKVLNLAREDIVWHSVSDLIQEVPGKVIDGLNMVEFAGDAVEVSEKLAALE 370

Query: 365  AFIQHLQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPP 424
            A +    +      +G+ + +   ++ ++Y MRK++VGLLG  +G  +P  F EDTAVPP
Sbjct: 371  AVLTEQINRGECGVVGYQVTQDKASIEKIYGMRKKAVGLLGATKGRRKPIAFAEDTAVPP 430

Query: 425  EQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALT 484
            E LADYI +FRALLD + L YGMFGHVDAGVLHVRPALDM D     L++ ISD VAALT
Sbjct: 431  EMLADYIMEFRALLDSHNLQYGMFGHVDAGVLHVRPALDMCDVEDEKLLRVISDQVAALT 490

Query: 485  KRYGGLLWGEHGKGLRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGL 543
             +YGGL+WGEHGKG+R EY P  FG ELY  LQ +KG FDP N+LNPGK+  P  +    
Sbjct: 491  LKYGGLMWGEHGKGVRGEYGPSVFGDELYGVLQDIKGLFDPDNRLNPGKLVAPKQAGGLC 550

Query: 544  TPVDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPK 603
              VD  T RG  DR I   V   +P  ++CNGNG C+NY     MCPS+K T +R  SPK
Sbjct: 551  FDVDS-TKRGKFDRQIPVEVRDAYPDVMNCNGNGLCFNYSSFSPMCPSFKVTGDRVQSPK 609

Query: 604  GRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQEDFSHEVYDAMA 663
            GRA LMREWLRL     +DV A AR K     G+  R++N     +   D+SHEV +++ 
Sbjct: 610  GRAGLMREWLRLLESEGVDVNALARAKP---LGILQRMQNT-INAKRDYDYSHEVMESLK 665

Query: 664  GCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYN 723
            GCLACK+C+ QCP+KV+VP FR++F  +Y+ RY RP +DYL+  +E ++P +A AP L N
Sbjct: 666  GCLACKACSSQCPVKVDVPKFRAQFFNIYYQRYLRPAKDYLVAGIEDSLPIMAAAPRLTN 725

Query: 724  AVMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVL 783
                +     ++   +G VD+P +S    +  L         + AL+ +   +R + +++
Sbjct: 726  FASQNPLSQWVIKKAIGYVDAPALSVPTLKQRLDGHASRGYDLAALQAIPADERAKFVLV 785

Query: 784  VQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQL 843
            VQD F  +++  L+  F+ L   LG +  L P+  NGKP H++GFL  FAK A  +A  L
Sbjct: 786  VQDPFNSFYDAGLVYRFVQLIETLGLKPVLLPFKPNGKPTHIKGFLDKFAKTAQSSADFL 845

Query: 844  KALADCGVPLVGLDPAMTLVYRQEYQKVPGL-EGCPKVLLPQEWLMDVLPEQAPAA--PG 900
              +   G+P+VG+DPA+ L YR EY+++ G   G  +V L  EWL+ +L +    A    
Sbjct: 846  NQVHKLGMPMVGIDPALVLCYRDEYKEILGANRGAFEVKLANEWLLSILQDIPTKAMQDK 905

Query: 901  SFRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIF 960
             F   +HCTE T  P +  +W ++F   G KL     GCCGM+GTYGHEA N E S+T+F
Sbjct: 906  QFTWFSHCTESTAKPNTANEWSKIFTHFGAKLTAVNLGCCGMAGTYGHEAENLERSKTLF 965

Query: 961  EQSWATKLDK--DGEPLATGYSCRSQVKRMTERKMRHPLEVVLQ 1002
            + SW   L +    + L +GYSCRSQVKR    K +HPLE +L+
Sbjct: 966  DMSWKDTLSRIDASQVLVSGYSCRSQVKRFAGYKPKHPLEALLE 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: 2373
Number of extensions: 90
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)
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