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

GapMind for catabolism of small carbon sources

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

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Echvi_1069 Echvi_1069 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>FitnessBrowser__Cola:Echvi_1069
          Length = 801

 Score =  490 bits (1262), Expect = e-142
 Identities = 319/838 (38%), Positives = 441/838 (52%), Gaps = 77/838 (9%)

Query: 6   VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEG----PKNGIALR----------- 50
           ++KVA+LG+GVMG++IA H  N  V V+L D+  KE      K G++L            
Sbjct: 5   IQKVAILGSGVMGSRIACHFANIGVKVLLLDILPKEPNEAESKKGLSLEDKAVRNRLVNE 64

Query: 51  AIENLKKLSPAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAP 110
           A+E   K  P+P+  +  A  IQ  N++DD+  +K+ D VIE + ER+D K  LY+KV  
Sbjct: 65  ALEKTLKSKPSPIYDRAFADRIQTGNFDDDLPKIKDYDWVIEVVVERLDIKQSLYEKVEQ 124

Query: 111 HLASHAIFATNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQIL 170
           H     +  +NTSG+ +  L +G   D ++ FCG HFFNPPRY+ L+E+IP   T P I+
Sbjct: 125 HRKPGTLITSNTSGIPMQMLCEGRSDDFQANFCGTHFFNPPRYLRLLEIIPGPKTDPAII 184

Query: 171 DQLEAFLTTTLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLG 230
           D L  +    LGK  V  KDTP FIANR+G++++++     E   +    VD LTG+ +G
Sbjct: 185 DFLMDYGDRHLGKETVLCKDTPAFIANRIGVYAMMSSMHIIESMKMGVSEVDKLTGTVIG 244

Query: 231 RAKSATFRTADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAG 290
           RAKSATFRT DVVGLDTM +V   +   L +D     +K P  +  L +   LG KTG G
Sbjct: 245 RAKSATFRTMDVVGLDTMVNVANNLSKALQNDESKDKFKLPKTVAYLSEKKWLGDKTGQG 304

Query: 291 FY-----KKEGKAIKVLDAKTGQYVDAGK-KADEIVVRMLKKDAAERIKLLRESTNPQAQ 344
           F+     K   K +K +D +T +Y  A K K   +       D  ERIK L    +    
Sbjct: 305 FFHMIRHKDGSKELKEIDLQTHEYKPAEKPKFKALEASKEINDLKERIKFLVNFDDEAGA 364

Query: 345 FLWAVFRDVFHYIAVYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQV------- 397
           F  A F D+F Y +  + +I+     ID A+  GFGW  GPFE+W   G K         
Sbjct: 365 FYRATFYDLFRYCSFRIPEISDELYRIDQAVCAGFGWEYGPFENWDILGLKDTIKKMEEA 424

Query: 398 ----AEWVKEDVEAGKALSAAPLPAWVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPV 453
               AEW+ E ++AG          +  E    +   + + +    P  Q F+    L  
Sbjct: 425 DQRPAEWIYEMLDAGNE------HFYRVEDGRRQYYDIPSKSYKDIPGQQEFILLDTL-- 476

Query: 454 YQRQAFRAAIKGTAAADPRKAGRTVEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVID 513
              +A    I G A A     G                 D+V+ + F +KMN++G +VI+
Sbjct: 477 ---KAANKKIWGNAGATIYDMG-----------------DEVIGLEFHTKMNSLGQEVIE 516

Query: 514 GLTRAIDLAEAGYKGLVVWQPTSLQLGAPGGPFSAGANLEAAMPAFMMGGAK---GIEPF 570
           G+  AI +AE  YKGLV+        G  G  FSAGANL      FM  G +    I   
Sbjct: 517 GINTAITMAEKDYKGLVI--------GNEGANFSAGANLAM---LFMFAGDQEFDEINLM 565

Query: 571 VKRFQDGMMRVKYASVPVVSAASGIALGGGCELMLHSASRVAALETYIGLVEVGVGLVPA 630
           + +FQ  MMRV+Y+SVPVV A   +ALGGGCE+ LH+ +  A  E Y+GLVE GVGL+PA
Sbjct: 566 IAQFQKTMMRVRYSSVPVVVAPHNMALGGGCEMSLHADAVQAHAELYMGLVEFGVGLIPA 625

Query: 631 GGGLKEAALAAARAAQAAGSTNILQFLTSRFQSAAMAKVSASALEARQMGYLQPSDKIVF 690
           GGG KE  L  + A   +G   + + L   F + A AKVS SA EAR +GYLQ  D I  
Sbjct: 626 GGGTKEMILRFSNAIH-SGDVEVNR-LQEYFMNIATAKVSTSAEEARGLGYLQAKDDITL 683

Query: 691 NVHELLYVAQNEVRALASAGYRAPL-PTLVPVAGRSGIATIKASLVNMRDGGFISTHDFL 749
           N       A+ +V  L   GY  P+  T + V G++ +A  +A +  MR G +IS HD  
Sbjct: 684 NRKRQFAEAKAKVIELFDEGYTQPVQQTNIKVLGKTSLALFEAGITGMRYGAYISEHDAK 743

Query: 750 IASRIAEAVCGGDVEAGSLVSEDWLLALERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           IA ++A  + GGD+   + VSE +LL LER+AF+ L G  KT ERI  +L  GKP+RN
Sbjct: 744 IARKLAWVMSGGDLSQANEVSEQYLLELEREAFLSLTGEQKTLERIQSILFKGKPLRN 801


Lambda     K      H
   0.319    0.134    0.391 

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: 1267
Number of extensions: 52
Number of successful extensions: 8
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: 807
Length of database: 801
Length adjustment: 41
Effective length of query: 766
Effective length of database: 760
Effective search space:   582160
Effective search space used:   582160
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: 56 (26.2 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