Alignments for a candidate for ech in Croceitalea dokdonensis DOKDO 023

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Croceitalea dokdonensis DOKDO 023

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_054557393.1 I595_RS00285 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_001306415.1:WP_054557393.1
          Length = 801

 Score =  462 bits (1189), Expect = e-134
 Identities = 310/829 (37%), Positives = 438/829 (52%), Gaps = 59/829 (7%)

Query: 6   VKKVAVLGAGVMGAQIAAHLINARVPVVLFD-----LPAKEGPK----------NGIALR 50
           + K+AV+G+G+MG+ IA H  N  V V+L D     L AKE  K          N I   
Sbjct: 5   INKIAVIGSGIMGSGIACHFANIGVEVLLLDIVPRELNAKEKAKGLTLDDTTVRNRIVND 64

Query: 51  AIENLKKLSPAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAP 110
           ++    K  P+P+  ++ A  I   N EDDIA + + D +IE + ER+D K  +++ +  
Sbjct: 65  SLAAALKSKPSPVYHQKFANRITTGNLEDDIAKVAKVDWIIEVVVERLDIKKQVFETLER 124

Query: 111 HLASHAIFATNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQIL 170
           H     +  +NTSG+ I  +S+G   D +  FCG HFFNP RY+ L E+IP   T P++L
Sbjct: 125 HRTPGTLITSNTSGIPIHFMSEGRSDDFQKHFCGTHFFNPARYLKLFEIIPGPKTSPEVL 184

Query: 171 DQLEAFLTTTLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLG 230
             L  +    LGK  V AKDTP FI NR+GIFSI ++F   +  G+  + VD LTG  +G
Sbjct: 185 VFLNGYGEQFLGKTSVLAKDTPAFIGNRIGIFSIQSLFHALKALGMTVEEVDKLTGPVIG 244

Query: 231 RAKSATFRTADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAG 290
           R KSATFRT DVVGLDT+ HV   + +   DD    ++  P  +  +++   LG KTG G
Sbjct: 245 RPKSATFRTVDVVGLDTLVHVANGISENCKDDERHELFALPDFIATMMENKWLGSKTGQG 304

Query: 291 FYKKEGKA-----IKVLDAKTGQYVDAGKKADEIVVRMLK--KDAAERIKLLRESTNPQA 343
           FYKK   A     I  LD  T +Y  + K A    +   K      +R  +L   T+   
Sbjct: 305 FYKKSKDAKGKTEILTLDLDTMEY-RSKKSAKFPTLEQTKTIDTVVDRFAVLTAGTDKAG 363

Query: 344 QFLWAVFRDVFHYIAVYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKE 403
           +F    F  +F Y++  + +I+     ID A++ GFGW  GPF+ W + G  +  E++  
Sbjct: 364 EFYRKSFGQLFAYVSHRIPEISDELYKIDDAMKAGFGWEHGPFQIWDAIGLDKGLEFI-- 421

Query: 404 DVEAGKALSAAPLPAWVFEGPVAENQGVHAAAGSWSPATQSFVARSK--LPVYQRQAFRA 461
              A +   AA   AWV E   A   G+ +       AT  +   SK  + V  + AF  
Sbjct: 422 ---AAEKQEAA---AWVSEMKTA---GITSFYQVKDGATYFYDIPSKQMVKVPGQDAF-- 470

Query: 462 AIKGTAAADPRKAGRTVEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDL 521
                   D  +  + V +N  V I   +  D +L   F+SKMNTIG DV+ GL +AIDL
Sbjct: 471 -----IILDNIRTTKEVFKNAGVVI--EDLGDGILNCEFQSKMNTIGADVLAGLNKAIDL 523

Query: 522 AEAGYKGLVVWQPTSLQLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRV 581
           AE  ++GLVV        G     FS GAN+       +      +   +K FQD MMR+
Sbjct: 524 AEKDFQGLVV--------GNQAANFSVGANIGMIFMMAVEQEYDELNMAIKMFQDSMMRM 575

Query: 582 KYASVPVVSAASGIALGGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAA 641
           +Y+S+P V+A  G+ LGGGCEL LH+   VAA ETY+GLVE GVG++P GGG KE A+ A
Sbjct: 576 RYSSIPTVAAPHGMTLGGGCELSLHADKVVAAAETYMGLVEFGVGVIPGGGGSKELAMRA 635

Query: 642 ARAAQAAG-STNILQFLTSRFQSAAMAKVSASALEARQMGYLQP-SDKIVFNVHELLYVA 699
           + + +      N+LQ     F +  MAKVS SA EA  +G LQ   D +V N    +  A
Sbjct: 636 SDSFRKGDVELNVLQ---EYFLTIGMAKVSTSAYEAYDLGLLQKGKDIVVVNKDRQIATA 692

Query: 700 QNEVRALASAGY-RAPLPTLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAV 758
           +   + +A AGY R P    V V G+  +        +M    +IS HD  IA+++A  +
Sbjct: 693 KAHAKLMAEAGYTRPPARKDVKVLGKQALGMFLVGTDSMEASNYISEHDKKIANKLAYVM 752

Query: 759 CGGDVEAGSLVSEDWLLALERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
            GGD+   ++VSE +LL +ER+AF+ L    KT ERI  ML+TGKP+RN
Sbjct: 753 AGGDLSEPTMVSEQYLLDIEREAFLSLCTERKTLERIQHMLKTGKPLRN 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: 1323
Number of extensions: 63
Number of successful extensions: 6
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: 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 24 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 2024 update 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