GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6937930
          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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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:

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:

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:

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:

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