Alignments for a candidate for ydiJ in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for ydiJ in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-hydroxyglutarate oxidase (EC 1.1.3.15) (characterized)
to candidate Echvi_3865 Echvi_3865 FAD/FMN-containing dehydrogenases

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



>FitnessBrowser__Cola:Echvi_3865
          Length = 982

 Score =  418 bits (1074), Expect = e-120
 Identities = 312/1032 (30%), Positives = 490/1032 (47%), Gaps = 96/1032 (9%)

Query: 12   ANYPEFLEALRNSGFRGQISADYATRTVLATDNSIYQRLPQAAVFPLDADDVARVATLMG 71
            AN   FL  L      G    D   +T+ ATD S+Y+ +P A   P    D+ +   L+ 
Sbjct: 6    ANLSPFLVGLAKE-LEGDFYYDQLMKTLYATDASVYREMPLAVAMPKTKGDIKK---LIH 61

Query: 72   EPRFQQVKLTPRGGGTGTNGQSLTDGIVVDLSRHMNNILEINVEERWVRVQAGTVKDQLN 131
                 +  L PR  GT   GQ + DGIVVD+S++   ILE N EE WVRVQ G V+D+LN
Sbjct: 62   FANTHKTSLIPRTAGTSLAGQCVGDGIVVDVSKYFTKILEFNKEEGWVRVQPGVVRDELN 121

Query: 132  AALKPHGLFFAPELSTSNRATVGGMINTDASGQGSCTYGKTRDHVLELHSVLLGGERLHS 191
            A LKPHG FF+P  ST+NRA +GGM+  ++ G  S  YG TR+H LEL ++L  G  +  
Sbjct: 122  AFLKPHGYFFSPVTSTANRAMIGGMVGNNSCGTTSIIYGSTREHTLELQTILSDGSEVTF 181

Query: 192  LPIDDAALEQACAAPGRVGEVYR-MAREI-QETQAELIETTFPK--LNRCLTGYDLAHL- 246
              +  A  E+        G++YR +  E+ Q  Q E I   FPK  + R  TGY + +L 
Sbjct: 182  RALSKAEFEEKKKLETLEGKLYREIYHELSQPEQQENIRKQFPKPSIQRRNTGYAVDYLL 241

Query: 247  -----RDEQGRFNLNSVLCGAEGSLGYVVEAKLNVLPIP-KYAVLVNVRYTSFMDALRDA 300
                  +    F+   +LCG+EG+L +  E K+++ P+P    V+V   + +  ++++  
Sbjct: 242  ETAVFSEHDTAFDFCKLLCGSEGTLAFTTEIKIHLDPLPAPKDVVVAAHFGTIHESMKAT 301

Query: 301  NALMAHKPLSIETVDSKVLMLAMKDIVWHSVAEYF-PADPERPTLGINLVEFCGDEPAEV 359
               M H P + E +D K+++   K+ +  S   YF   DPE    GI +VEF  +     
Sbjct: 302  QLAMKHFPTACELMD-KIILDCTKENIEQSKNRYFVEGDPE----GILMVEFRDETEEGA 356

Query: 360  NAKVQAFIQHLQSDTSVERLGHTL-AEGAEAVTRVYTMRKRSVGLLGNVEGEVRPQPFVE 418
              + Q  I  +++      LG+       E    V+T+R   +GLL N+ G+ +    +E
Sbjct: 357  LGQAQKMIDAMKA----AGLGYAYPIITGERTKNVWTLRSAGLGLLANIPGDRKAVACIE 412

Query: 419  DTAVPPEQLADYIADFRALLDGYGLAYGMFGHVDAGVLHVRPALDMKDPVQAALVKPISD 478
            DTAV  + LAD+I +F  ++ G+G     + H  AG +H+RP LD+K          I++
Sbjct: 413  DTAVDIDDLADFIDEFGEIMKGFGQKPVHYAHAGAGEIHLRPILDLKKSEDVEDFYKITE 472

Query: 479  AVAALTKRYGGLLWGEHGKG-LRSEYVPEYFG-ELYPALQRLKGAFDPHNQLNPGKI--C 534
            AVA L K+Y G L GEHG G +R+ ++P   G E Y   +R+K ++DP+   NPGKI   
Sbjct: 473  AVAKLVKKYDGSLSGEHGDGRVRAAFIPIMVGEENYQLFRRIKQSWDPNAIFNPGKIVDT 532

Query: 535  TPLGSAEGLTPVDGVTLRGDLDRTID-ERVWQDFPSAVHCNGNGACYNYD-PNDAMCPSW 592
             P+ S       +   +  + + T+D   V     +A  CNG+G C         MCPS+
Sbjct: 533  APMNS---FLRYERDMVTPEFETTMDFGHVGGILRAAEKCNGSGDCRKLPVSGGTMCPSY 589

Query: 593  KATRERQHSPKGRASLMREWLRLQGEANIDVLAAARNKVSWLKGLPARLRNNRARNQGQE 652
             AT+  + + +GRA+ +RE+L                                 +N    
Sbjct: 590  MATKNERDTTRGRANTLREFL--------------------------------TKNTQPN 617

Query: 653  DFSH-EVYDAMAGCLACKSCAGQCPIKVNVPDFRSRFLELYHGRYQRPLRDYLIGSLEFT 711
             F H E+ + M  CL+CK C  +CP  V++   ++ FL  YH  +  PLR      +   
Sbjct: 618  PFDHPEIKEVMDLCLSCKGCTSECPSNVDMSSLKAEFLHQYHKTHGIPLRSKAFAYINNL 677

Query: 712  IPYLAHAPGLYNAVMGSKWVSQLLADKVGMVDS---PLISRFNFQATLTRCRVGMATVPA 768
                +  PG+ N +M +K    ++   +G+ +    P I++ N +    +       +PA
Sbjct: 678  NELGSLVPGMTNFLMTNKATGNMMKKVLGVAEKRQLPTIAKVNLRKWYNK---HYGNLPA 734

Query: 769  LRELTPAQRERSIVLVQDAFTRYFETPLLSAFIDLAHRLGHRVFLAPYSANGKPLHVQGF 828
                 P+++  ++    D FT + +T +    I L H LG+ V LA +  +G+    +G 
Sbjct: 735  -----PSKKVGAVHFFCDEFTNFNDTEIGIKAIQLLHHLGYEVKLADHPESGRGAISKGL 789

Query: 829  LGAFAKAAIRNATQLKALADCGVPLVGLDPAMTLVYRQEYQKVPG---LEGCPKV----L 881
            L    K A +N    K       PLVG++P+  L ++ EY ++     +E   K+    +
Sbjct: 790  LDRAKKLANQNVQLFKDKVTLDEPLVGVEPSAILTFKDEYPRLVDKYLVEDAKKLKRHSM 849

Query: 882  LPQEWLM------DVLPEQAPAAPGSFRLMAHCTEKTNVPASTRQWEQVFARLGLKLVTE 935
            +  E+L       ++  +Q   A     L  HC +K+    S  Q + +       L T 
Sbjct: 850  MVDEFLAKEAMRGNISADQFTKAHKKVLLHGHCHQKSLSSVSFTQ-KLLTLPENYTLETI 908

Query: 936  ATGCCGMSGTYGHEARNQETSRTIFEQ---SWATKLDKDGEPLATGYSCRSQVKRMTERK 992
             +GCCGM+G++G+E  + E S  + E        K DK     A G SCR Q+   T RK
Sbjct: 909  PSGCCGMAGSFGYEEEHYEVSMNVGELVLFPTIRKADKATVVAAPGTSCRHQIADGTGRK 968

Query: 993  MRHPLEVVLQYA 1004
              HP+EV+   A
Sbjct: 969  ALHPVEVLFDAA 980


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: 2081
Number of extensions: 107
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1006
Length of database: 982
Length adjustment: 44
Effective length of query: 962
Effective length of database: 938
Effective search space:   902356
Effective search space used:   902356
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