Alignments for a candidate for ech in Azohydromonas australica DSM 1124

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Azohydromonas australica DSM 1124

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_029001171.1 H537_RS0132195 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000430725.1:WP_029001171.1
          Length = 796

 Score = 1012 bits (2616), Expect = 0.0
 Identities = 518/807 (64%), Positives = 613/807 (75%), Gaps = 11/807 (1%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MS F V+K AVLGAGVMGAQIAA+ IN RVPVVLFDLPAKEGPKN I  +A++NLKKL P
Sbjct: 1   MSRFQVRKAAVLGAGVMGAQIAANFINVRVPVVLFDLPAKEGPKNAIVTKAVDNLKKLKP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           APLG+ EEAGLI+ ANYE D+ALL ECDLVIEAIAERMDWK  LY ++APH+A HAI A+
Sbjct: 61  APLGLAEEAGLIRQANYEQDLALLAECDLVIEAIAERMDWKQQLYAQIAPHVAPHAIVAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSIT LS     +L+ RFCG+HFFNPPRYM LVELIP   T P+ILDQLE F+TT 
Sbjct: 121 NTSGLSITQLSQALPEELRPRFCGIHFFNPPRYMQLVELIPAPQTAPEILDQLETFVTTG 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGVVRAKDTPNF+ANRVG+ ++LA   EAE+F + +DVVDDLTG KLGRA S TFRTA
Sbjct: 181 LGKGVVRAKDTPNFVANRVGVMNMLATMVEAERFKLSYDVVDDLTGKKLGRASSGTFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDT+AHV++TMQ+ L DDPF   + TP VL GL+  GALGQK GAGFY+K GK I 
Sbjct: 241 DVVGLDTLAHVVRTMQEQLPDDPFKAHFATPPVLAGLIAQGALGQKAGAGFYRKVGKDIL 300

Query: 301 VLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360
            LD +   YV +G KADEIV RMLKK  AER+KLLRES+NPQAQFLWA+ RD FHY AV+
Sbjct: 301 RLDPEKRDYVPSGAKADEIVGRMLKKPPAERLKLLRESSNPQAQFLWAILRDGFHYAAVH 360

Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420
           L  IA SA ++DLA+RWGFG   GPFE WQSAGW QVA+W+KED++AGKALS+APLPAWV
Sbjct: 361 LADIADSAREVDLALRWGFGMAQGPFELWQSAGWTQVAQWIKEDIDAGKALSSAPLPAWV 420

Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480
           FEGPVAE  GVH A GSWS A  SFV   +LPVY+RQ F  ++ G    D  K+G  + +
Sbjct: 421 FEGPVAERGGVHTAEGSWSAAQGSFVPPRELPVYERQLFPESVAG-LGRDALKSGTELFK 479

Query: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLG 540
              +R+W  +G  +VL+ S  SK++ I PDV  GLT+A++LAE  +K LV+W P  +   
Sbjct: 480 GPELRVWTLDG--EVLIASITSKLHLISPDVTAGLTKAVELAEQQFKALVIWSPDEM--- 534

Query: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGG 600
                FSAGANLEA MP FM  G  GI P  ++ Q  M+RV+YA VPVV+A  GIALGGG
Sbjct: 535 -----FSAGANLEALMPVFMAKGPAGIGPEEQKMQQLMLRVRYAGVPVVAAMRGIALGGG 589

Query: 601 CELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSR 660
           CEL +H A RVAA+ETY+GLVEVGVGL+P  GGL   A  AA    AA +T++L FL   
Sbjct: 590 CELAVHCARRVAAMETYVGLVEVGVGLLPGAGGLTYIARRAAEKGAAAPNTDLLAFLKDG 649

Query: 661 FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPTLVP 720
           + +AA A V  SALE+R++GYL  SD IV +  ELLYVA NE +ALA +GYR PL    P
Sbjct: 650 YMAAATATVGTSALESRKLGYLLESDVIVPHKDELLYVALNEAKALADSGYRPPLKRSFP 709

Query: 721 VAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALERK 780
           VAGRSGIATI+A LV MRDGGFIS HD+ I   IAE VCGG+++AG+LV+E++L+ALERK
Sbjct: 710 VAGRSGIATIEAQLVGMRDGGFISAHDYRIGRLIAEVVCGGELDAGTLVTEEYLMALERK 769

Query: 781 AFVDLLGTGKTQERIMGMLQTGKPVRN 807
            F  LLG  KTQERIMGMLQTGKPVRN
Sbjct: 770 HFCGLLGHPKTQERIMGMLQTGKPVRN 796


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: 1619
Number of extensions: 52
Number of successful extensions: 4
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: 796
Length adjustment: 41
Effective length of query: 766
Effective length of database: 755
Effective search space:   578330
Effective search space used:   578330
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: 55 (25.8 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 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