Aligments for a candidate for ydiJ in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for ydiJ in Shewanella amazonensis SB2B

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate 6937930 Sama_2071 oxidoreductase, FAD-binding, putative (RefSeq)

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



>lcl|FitnessBrowser__SB2B:6937930 Sama_2071 oxidoreductase,
            FAD-binding, putative (RefSeq)
          Length = 1007

 Score =  899 bits (2323), Expect = 0.0
 Identities = 475/1001 (47%), Positives = 646/1001 (64%), Gaps = 22/1001 (2%)

Query: 14   YPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEP 73
            Y  FLEAL  + F G+I   Y+ R V ATDNS+YQ LPQA ++P    DV RV  L  + 
Sbjct: 15   YLAFLEALA-ADFDGEIDTRYSARIVQATDNSVYQFLPQAVLYPKSTLDVQRVMQLAAKD 73

Query: 74   RFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAA 133
             F++V  + RGGGTGTNGQSLT G+++DLSRHMN +LE+N EE W RV+AG VKD LN A
Sbjct: 74   EFREVVFSARGGGTGTNGQSLTHGLILDLSRHMNKVLEVNAEEGWARVEAGVVKDALNDA 133

Query: 134  LKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLP 193
            L+PHG FF+P+LSTSNRAT+GGMINTDASG GS  YGKT DHVL L SVL+ G  L S+P
Sbjct: 134  LRPHGFFFSPDLSTSNRATLGGMINTDASGAGSLVYGKTSDHVLGLKSVLIDGSVLDSVP 193

Query: 194  IDDAALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDLAHLRDEQ-GR 252
            +   +L+    +    G++      +   + EL++T FP+LNR LTGYDL H+ D+   +
Sbjct: 194  MAAESLD-TVDSRSLAGKLIANISAVCRDKRELVKTRFPRLNRFLTGYDLEHVWDDDLSQ 252

Query: 253  FNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLSIE 312
            F+L+ +L G+EG+L  + EAK+N+ P+PK   +VN++Y SF  ALR A +L+A     +E
Sbjct: 253  FDLSRILTGSEGTLAVITEAKVNLTPLPKQRAMVNIKYDSFESALRHAPSLVAASATVVE 312

Query: 313  TVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAK---VQAFIQH 369
            TVDSKVL LA +DIVWHSV+E     P +   G+N+VEF GDE AEVNAK   ++A +  
Sbjct: 313  TVDSKVLGLAREDIVWHSVSELIQEVPGKHIDGLNMVEFAGDE-AEVNAKLAALEAVLAE 371

Query: 370  LQSDTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLAD 429
               +     +G        ++ ++Y MRK++VGLLG  +G  +P  F EDTAVPPE+LAD
Sbjct: 372  QIKNGECGVVGFRSTHDKVSIEKIYAMRKKAVGLLGAAKGSRKPIAFAEDTAVPPEKLAD 431

Query: 430  YIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGG 489
            +I +FRALLDG+ L YGMFGHVDAGVLHVRPALDM DPV   L++ ISD VAALT +YGG
Sbjct: 432  FIMEFRALLDGHKLQYGMFGHVDAGVLHVRPALDMCDPVDEKLLRTISDEVAALTLKYGG 491

Query: 490  LLWGEHGKGLRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGLTPVDG 548
            L+WGEHGKG+R EY P  FG ELY  LQ +KG FDP N+LNPGK+  P    E    VD 
Sbjct: 492  LMWGEHGKGVRGEYGPAVFGDELYGVLQDIKGWFDPDNRLNPGKLVAPKDKGELFYNVDS 551

Query: 549  VTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPKGRASL 608
               RG  DR I  +V + FP  ++CNGNG C+NY     MCPS+K T +R  SPKGR+SL
Sbjct: 552  AK-RGSFDRQIPVKVREAFPDVMNCNGNGLCFNYSAYSPMCPSFKVTGDRIQSPKGRSSL 610

Query: 609  MREWLRLQGEANIDVLAAARNK-VSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAGCLA 667
            MREWLRL     +DV   A++K + WL     +   N  + + + D+SHEV +++ GCLA
Sbjct: 611  MREWLRLLEAEGVDVEQLAKSKPLGWL-----QRAQNSLKAKDEYDYSHEVMESLKGCLA 665

Query: 668  CKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMG 727
            CK+C+GQCP+KV+VP FR++F  +Y+ RY RP +DYL+  +E  +P +A AP L NA+  
Sbjct: 666  CKACSGQCPVKVDVPKFRAQFFNIYYQRYLRPPKDYLVAGIEDALPLMAKAPKLVNALSQ 725

Query: 728  SKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDA 787
            +     ++   +G VD+P +S       L   +     + +L+ +  A+R R +++ QD 
Sbjct: 726  NSLSQWVIKKAIGYVDAPKLSVPTLTQRLESHQSLGYDLESLKRIPAAERSRYVLVAQDP 785

Query: 788  FTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLKALA 847
            F  +++  L+  F+ L  +LG +  L P+  NGKP H++GFL  FA +A   A     L 
Sbjct: 786  FNSFYDAGLVYHFVKLIEKLGFKPVLLPFKPNGKPAHIKGFLDKFAASAGTAAAFFNELG 845

Query: 848  DCGVPLVGLDPAMTLVYRQEYQKVPGLE-GCPKVLLPQEWLMDV---LPEQAPAAPGSFR 903
              G+P+VG+DPAM LVYR EY+   G + G   + L  EWLM+V   LP++  +  G + 
Sbjct: 846  KLGMPMVGVDPAMVLVYRDEYKVALGKDRGDFNIKLANEWLMEVLEALPQRELSGRG-YT 904

Query: 904  LMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIFEQS 963
              +HCTE T  P + ++W  +FAR G  L  +  GCCGM+GTYGHE  N   S+ +++ S
Sbjct: 905  WFSHCTESTAKPGTAKEWSAIFARFGATLKVKNLGCCGMAGTYGHELDNLARSQQLYDMS 964

Query: 964  WATKLDKDG--EPLATGYSCRSQVKRMTERKMRHPLEVVLQ 1002
            W   ++     E L +GYSCRSQVKR +  + +HPLE +L+
Sbjct: 965  WKEGINGTSREEILVSGYSCRSQVKRFSGFRPKHPLEALLE 1005


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: 2367
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: 1007
Length adjustment: 45
Effective length of query: 961
Effective length of database: 962
Effective search space:   924482
Effective search space used:   924482
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, or view the source code.

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