Alignments for a candidate for ydiJ in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Shewanella loihica PV-4

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate 5209072 Shew_1550 FAD linked oxidase domain-containing protein (RefSeq)

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



>FitnessBrowser__PV4:5209072
          Length = 1026

 Score =  899 bits (2323), Expect = 0.0
 Identities = 478/1014 (47%), Positives = 649/1014 (64%), Gaps = 34/1014 (3%)

Query: 14   YPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEP 73
            Y  FL+AL  S + G I   Y+ R   ATDNS+YQ LPQA ++P    DV  + TL  +P
Sbjct: 15   YLAFLDALAQSNYCGDIDKRYSARLAQATDNSVYQFLPQAVLYPKTQADVKLIMTLATKP 74

Query: 74   RFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAA 133
             F+QV  + RGGGTGTNGQSLT G+++DLSR+ N ++EIN +ERWVRVQAG VKD LN A
Sbjct: 75   EFKQVVFSARGGGTGTNGQSLTHGLILDLSRYFNQVIEINEKERWVRVQAGVVKDALNDA 134

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

Query: 194  IDDAALE--QACAAPGRVGEVYR-MAREIQETQAELIETTFPKLNRCLTGYDLAHLRDEQ 250
            +D  ALE   A  +P     + R +AR  +E + E +E+ FPKLNR LTGYDL ++ +E 
Sbjct: 195  LDLKALEALDALESPSLGQSLQRDIARMTREHRGE-VESRFPKLNRFLTGYDLKNVWNET 253

Query: 251  -GRFNLNSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPL 309
               FNL+ +L G+EG+L  + EAKL++ P+PK  ++VN++Y SF  ALR A  L+  +  
Sbjct: 254  VDEFNLSRILTGSEGTLAVITEAKLDITPLPKTRMMVNIKYDSFQSALRHAPDLVKAEVT 313

Query: 310  SIETVDSKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAKVQAFIQH 369
             +ETVDSKVL LA +DI+WHSV+      P     G+N+VEF G EP EV AKV+     
Sbjct: 314  VVETVDSKVLNLAKQDIIWHSVSSLIEDVPGASIDGLNMVEFAG-EPDEVEAKVKQLEAM 372

Query: 370  LQSDTSVER---LGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQ 426
            L +  +      LG+ +     ++  +Y MRK++VGLLG  +G  +P  F EDTAVPPE+
Sbjct: 373  LDTQLAANEAGLLGYQVTSDKASINTIYAMRKKAVGLLGATKGSRKPIAFAEDTAVPPEK 432

Query: 427  LADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKR 486
            LAD+I +FRALLD + L YGMFGHVDAGVLHVRPALDM DP    L+K +SD VAALT +
Sbjct: 433  LADFILEFRALLDSHELQYGMFGHVDAGVLHVRPALDMCDPQDERLLKTVSDQVAALTLK 492

Query: 487  YGGLLWGEHGKGLRSEYVPEYFGE-LYPALQRLKGAFDPHNQLNPGKICTPLGSAEGLTP 545
            YGGL+WGEHGKG+R EY P  FGE L+  L+ +KG FDP+N+LNPGK+  P GS   L  
Sbjct: 493  YGGLMWGEHGKGVRGEYGPSVFGETLFGLLEEVKGYFDPNNKLNPGKLVAPKGSGPLLYN 552

Query: 546  VDGVTLRGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPKGR 605
            VD  T RG  DR I     + FP  ++CNGNG C+NY     MCPS+K T +R  SPKGR
Sbjct: 553  VDS-TKRGAFDRQIPVNTREAFPDVMNCNGNGLCFNYSVYSPMCPSFKVTGDRVQSPKGR 611

Query: 606  ASLMREWLRLQGEANIDVLAAARNK-VSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAG 664
            A LMREWLRL     +DV A A+ K + WL+     L+  R     + D+SHEV +++ G
Sbjct: 612  AGLMREWLRLLEAEGVDVEALAKAKPLGWLQRTQNTLKKER-----EYDYSHEVMESLKG 666

Query: 665  CLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNA 724
            CLACK+C+ QCP+KV+VP FR++F  +Y+ RY RP++DYL+  +E ++P +A  P + N 
Sbjct: 667  CLACKACSSQCPVKVDVPKFRAQFFNIYYQRYLRPVKDYLVAGIEESLPLMAKVPQITNF 726

Query: 725  VMGSKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLV 784
               +K    ++   +G VD+P +S    +  L         + AL+++  A+R++ +++V
Sbjct: 727  ASQNKLSQWVIKQSIGYVDAPALSVPTLKQRLENHACRGYDLNALQQIPEAERDQYVLVV 786

Query: 785  QDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLK 844
            QD F  ++E   +  FI L  +LG +  L P+  NGKP+H++GFL  FAK A  +A  L 
Sbjct: 787  QDPFNSFYEAETVYHFIKLIEKLGFKPVLLPFKPNGKPIHIKGFLDKFAKTAQSSADFLN 846

Query: 845  ALADCGVPLVGLDPAMTLVYRQEYQKV-PGLEGCPKVLLPQEWLMDVLPEQAPAAPGS-- 901
             +   G+P+VG+DPAM L YR EY+++     G   VLL  EWL+ V+   AP A  +  
Sbjct: 847  QVHALGMPMVGVDPAMVLCYRDEYKEILAENRGDFNVLLANEWLLKVIDIVAPTAKSAKL 906

Query: 902  ------------FRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHE 949
                        F   +HCTE T  P + ++W+ +F+  G +L T + GCCGM+GTYGHE
Sbjct: 907  NKSANATNANRQFTWFSHCTESTAKPNTAKEWQAIFSAFGAELSTVSLGCCGMAGTYGHE 966

Query: 950  ARNQETSRTIFEQSWATKLDK--DGEPLATGYSCRSQVKRMTERKMRHPLEVVL 1001
            + N + S+ ++E SW   +D     + L +GYSCRSQVKR    K +HP++ +L
Sbjct: 967  SDNLKRSKALYEMSWEKAIDSLPHEQILISGYSCRSQVKRFGGFKPKHPVQALL 1020


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: 2380
Number of extensions: 91
Number of successful extensions: 11
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: 1026
Length adjustment: 45
Effective length of query: 961
Effective length of database: 981
Effective search space:   942741
Effective search space used:   942741
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