Alignments for a candidate for paaH in Dechloromonas agitata is5

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaH in Dechloromonas agitata is5

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_027458118.1 K420_RS0111060 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000519045.1:WP_027458118.1
          Length = 799

 Score =  885 bits (2288), Expect = 0.0
 Identities = 455/811 (56%), Positives = 579/811 (71%), Gaps = 16/811 (1%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           M+  IVKK AVLGAGVMGAQIAAHL NA VPVVLFDLPAKEG KNGI  +A++ LKKL P
Sbjct: 1   MNKLIVKKAAVLGAGVMGAQIAAHLANANVPVVLFDLPAKEGDKNGIVKKALDGLKKLEP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           APL  K +   I AANY++ + LL ECDLVIEAIAERMDWK+DLY K+APH+ ++AI A+
Sbjct: 61  APLASKSKLKFIDAANYDEHLPLLAECDLVIEAIAERMDWKNDLYAKIAPHIGANAIVAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLS+ AL+ G    ++ RFCG+HFFNPPRYMHLVE+I T TT    LD LE +LT+ 
Sbjct: 121 NTSGLSMNALAQGLPESIRPRFCGIHFFNPPRYMHLVEIIGTQTTDGSTLDALETWLTSR 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGV+RA DTPNF+ANR+G+FSILAV    + FG+ FD VD LTG K+GR KSAT+RTA
Sbjct: 181 LGKGVIRALDTPNFVANRIGVFSILAVMHHTQAFGLGFDEVDALTGPKIGRPKSATYRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDT+AHV+KTMQDTL +DP+   + TPA LK L++ GALGQKT  G ++K+GK I+
Sbjct: 241 DVVGLDTLAHVVKTMQDTLPNDPWHAHFTTPAWLKLLIEKGALGQKTRCGIFRKQGKEIQ 300

Query: 301 VLDAKTGQY-VDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAV 359
           VLD     Y   AG+ A+E+   +  K  AE+   LR S++PQAQFLWA+FRD+FHY AV
Sbjct: 301 VLDLAAQDYRKSAGEIAEEVAAILKIKSPAEKFAALRASSHPQAQFLWAIFRDIFHYAAV 360

Query: 360 YLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAW 419
            LE +A +A D+DLA+RWGFGW  GPFE WQ+AGW  +A+ V  D+ AGK +++ PLPAW
Sbjct: 361 QLESVADNARDLDLAMRWGFGWAQGPFETWQAAGWSDIAQAVAADIAAGKTMASVPLPAW 420

Query: 420 VFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVE 479
             E   A   GVHAA GS+S +  ++V RS LPVYQRQ F   + G  AA P K+G T+ 
Sbjct: 421 ALE---AGRTGVHAAEGSYSASKNAYVPRSSLPVYQRQLFPERVLGEVAATPEKSGETLY 477

Query: 480 ENDAVRIWVSEGQD-DVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538
           EN+ VR+W     D  + ++S KSKM+TIG +V+DG+  A+  AE    G+VVW      
Sbjct: 478 ENEGVRLWRLPSLDAGIGILSVKSKMHTIGNEVLDGVIAAVKQAEGTLDGVVVWHE---- 533

Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598
                 PF+ GANL+    A   G    +E  V++FQ     +KYA VPVV+A  G+ALG
Sbjct: 534 -----APFAVGANLQQVGEACAAGQFDILEATVEKFQRASQTLKYAQVPVVAAVQGMALG 588

Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAAR-AAQAAGSTNILQFL 657
           GGCE ++H+  RV ALE+YIGLVE GVGL+PAGGG KE A+ AA  AAQ+A    +  FL
Sbjct: 589 GGCEFVMHAGKRVMALESYIGLVEAGVGLIPAGGGCKEFAVRAAEWAAQSATPGEVFNFL 648

Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYR-APLP 716
              FQ+ AMAKV+ SA+EA  MG+ +PSD I+FN +ELL+VA  E RA+A AGY   P+ 
Sbjct: 649 QPVFQTIAMAKVAKSAVEAIDMGFAKPSDTILFNANELLWVAIKEARAMADAGYAPPPMA 708

Query: 717 TLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLA 776
             V VAG++GIAT++  LVNM++GG IS HD+++A   A A+CGG+VE GS+V E+WL+ 
Sbjct: 709 RGVIVAGKNGIATLEMMLVNMKEGGMISAHDYVVARSAAVALCGGEVETGSVVDEEWLIT 768

Query: 777 LERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           +ER+ FV+LL    TQ RI  ML+TGKP+RN
Sbjct: 769 VERRLFVELLKNPLTQTRIKHMLETGKPLRN 799


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: 1566
Number of extensions: 53
Number of successful extensions: 7
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: 799
Length adjustment: 41
Effective length of query: 766
Effective length of database: 758
Effective search space:   580628
Effective search space used:   580628
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.

Downloads

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