Alignments for a candidate for ydiJ in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Escherichia coli BW25113

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate 15806 b1687 predicted FAD-linked oxidoreductase (NCBI)

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



>FitnessBrowser__Keio:15806
          Length = 1018

 Score =  980 bits (2533), Expect = 0.0
 Identities = 511/1000 (51%), Positives = 661/1000 (66%), Gaps = 16/1000 (1%)

Query: 17   FLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMGEPRFQ 76
            FL+ L   GF G  +  YA R  ++TDNSIYQ LP A VFP    DVA +A L  + R+ 
Sbjct: 18   FLQELEQQGFTGDTATSYADRLTMSTDNSIYQLLPDAVVFPRSTADVALIARLAAQERYS 77

Query: 77   QVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLNAALKP 136
             +  TPRGGGTGTNGQ+L  GI+VD+SRHMN I+EIN EE WVRV+AG +KDQLN  LKP
Sbjct: 78   SLIFTPRGGGTGTNGQALNQGIIVDMSRHMNRIIEINPEEGWVRVEAGVIKDQLNQYLKP 137

Query: 137  HGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHSLPIDD 196
             G FFAPELSTSNRAT+GGMINTDASGQGS  YGKT DHVL + +VLLGG+ L + P+  
Sbjct: 138  FGYFFAPELSTSNRATLGGMINTDASGQGSLVYGKTSDHVLGVRAVLLGGDILDTQPLPV 197

Query: 197  AALEQACAAPGRVGEVYRMAREIQETQAELIETTFPKLNRCLTGYDLAHL-RDEQGRFNL 255
               E    +   +G +Y    +    Q +LI   FPKLNR LTGYDL H+  DE   F+L
Sbjct: 198  ELAETLGKSNTTIGRIYNTVYQRCRQQRQLIIDNFPKLNRFLTGYDLRHVFNDEMTEFDL 257

Query: 256  NSVLCGAEGSLGYVVEAKLNVLPIPKYAVLVNVRYTSFMDALRDANALMAHKPLSIETVD 315
              +L G+EG+L ++ EA+L++  +PK   LVNV+Y SF  ALR+A  ++  + LS+ETVD
Sbjct: 258  TRILTGSEGTLAFITEARLDITRLPKVRRLVNVKYDSFDSALRNAPFMVEARALSVETVD 317

Query: 316  SKVLMLAMKDIVWHSVAEYFPADPERPTLGINLVEFCGDEPAEVNAKVQAF---IQHLQS 372
            SKVL LA +DIVWHSV+E     P++  LG+N+VEF GD+ A ++ +V A    +  L +
Sbjct: 318  SKVLNLAREDIVWHSVSELITDVPDQEMLGLNIVEFAGDDEALIDERVNALCARLDELIA 377

Query: 373  DTSVERLGHTLAEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVEDTAVPPEQLADYIA 432
                  +G  +      V R+Y MRK++VGLLGN +G  +P PF EDT VPPE LADYIA
Sbjct: 378  SHQAGVIGWQVCRELAGVERIYAMRKKAVGLLGNAKGAAKPIPFAEDTCVPPEHLADYIA 437

Query: 433  DFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISDAVAALTKRYGGLLW 492
            +FRALLD +GL+YGMFGHVDAGVLHVRPALDM DP Q  L+K ISD V ALT +YGGLLW
Sbjct: 438  EFRALLDSHGLSYGMFGHVDAGVLHVRPALDMCDPQQEILMKQISDDVVALTAKYGGLLW 497

Query: 493  GEHGKGLRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKICTPLGSAEGLTPVDGVTL 551
            GEHGKG R+EY P +FG EL+  L+++K AFDPHN+LNPGKIC P G    +  VD V  
Sbjct: 498  GEHGKGFRAEYSPAFFGEELFAELRKVKAAFDPHNRLNPGKICPPEGLDAPMMKVDAVK- 556

Query: 552  RGDLDRTIDERVWQDFPSAVHCNGNGACYNYDPNDAMCPSWKATRERQHSPKGRASLMRE 611
            RG  DR I   V Q +  A+ CNGNG C+N+D    MCPS K T+ R HSPKGRA+L+RE
Sbjct: 557  RGTFDRQIPIAVRQQWRGAMECNGNGLCFNFDARSPMCPSMKITQNRIHSPKGRATLVRE 616

Query: 612  WLRLQGEANIDVLAAAR----NKVSWLKGLPARLRNNRARNQGQEDFSHEVYDAMAGCLA 667
            WLRL  +  +D L   +    + VS L+ L AR RN+   N+G+ DFSHEV +AM+GCLA
Sbjct: 617  WLRLLADRGVDPLKLEQELPESGVS-LRTLIARTRNSWHANKGEYDFSHEVKEAMSGCLA 675

Query: 668  CKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFTIPYLAHAPGLYNAVMG 727
            CK+C+ QCPIK++VP+FRSRFL+LYH RY RPLRD+L+ ++E   P +A AP  +N  + 
Sbjct: 676  CKACSTQCPIKIDVPEFRSRFLQLYHTRYLRPLRDHLVATVESYAPLMARAPKTFNFFIN 735

Query: 728  SKWVSQLLADKVGMVDSPLISRFNFQATLTRCRVGMATVPALRELTPAQRERSIVLVQDA 787
               V +L    +GMVD PL+S  + Q  +   R    T+  L  L   Q+ R++++VQD 
Sbjct: 736  QPLVRKLSEKHIGMVDLPLLSVPSLQQQMVGHRSANMTLEQLESLNAEQKARTVLVVQDP 795

Query: 788  FTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGFLGAFAKAAIRNATQLKALA 847
            FT Y++  +++ F+ L  +LG +  L P+S NGK  H++GFL  FAK A + A  L  +A
Sbjct: 796  FTSYYDAQVVADFVRLVEKLGFQPVLLPFSPNGKAQHIKGFLNRFAKTAKKTADFLNRMA 855

Query: 848  DCGVPLVGLDPAMTLVYRQEYQKVPGLE-GCPKVLLPQEWLMDVLPEQ--APAAPGSFRL 904
              G+P+VG+DPA+ L YR EY+   G E G   VLL  EWL   L  Q  A  +  S+  
Sbjct: 856  KLGMPMVGVDPALVLCYRDEYKLALGEERGEFNVLLANEWLASALESQPVATVSGESWYF 915

Query: 905  MAHCTEKTNVPASTRQWEQVFARLGLKLVTEATGCCGMSGTYGHEARNQETSRTIFEQSW 964
              HCTE T +P +  QW  +FAR G KL   + GCCGM+GTYGHEA+N E S  I+E SW
Sbjct: 916  FGHCTEVTALPGAPAQWAAIFARFGAKLENVSVGCCGMAGTYGHEAKNHENSLGIYELSW 975

Query: 965  ATKLDK--DGEPLATGYSCRSQVKRMTERKMRHPLEVVLQ 1002
               + +      LATGYSCRSQVKR+    +RHP++ +L+
Sbjct: 976  HQAMQRLPRNRCLATGYSCRSQVKRVEGTGVRHPVQALLE 1015


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: 2354
Number of extensions: 96
Number of successful extensions: 8
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: 1018
Length adjustment: 45
Effective length of query: 961
Effective length of database: 973
Effective search space:   935053
Effective search space used:   935053
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