Alignments for a candidate for ech in Polaromonas naphthalenivorans CJ2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Polaromonas naphthalenivorans CJ2

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011802844.1 PNAP_RS17360 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000015505.1:WP_011802844.1
          Length = 810

 Score =  985 bits (2547), Expect = 0.0
 Identities = 511/818 (62%), Positives = 609/818 (74%), Gaps = 19/818 (2%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MS+F VKKVAVLGAGVMGAQIAAHL+N RVPVVLFDLPA++GPKNGI  +AIE LKKL P
Sbjct: 1   MSSFQVKKVAVLGAGVMGAQIAAHLVNCRVPVVLFDLPARDGPKNGIVSKAIEGLKKLKP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           APLG+ E+A LIQ ANYE+ + +LKECDL+IEAIAERMDWK DLY K+AP +A  AI A+
Sbjct: 61  APLGVVEDAALIQQANYEEHMDVLKECDLIIEAIAERMDWKTDLYHKIAPFVAEGAIVAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSIT LS+     LK RFCG+HFFNPPRYM LVELI T TT+  +LD LEAF+TT 
Sbjct: 121 NTSGLSITTLSEALPDSLKPRFCGIHFFNPPRYMALVELINTPTTEAAVLDDLEAFVTTA 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGV+RA DTPNFIANRVGI  +LA   EA+ FG+ +DVVDDLTG KLGRA S TFRTA
Sbjct: 181 LGKGVIRAHDTPNFIANRVGIAGMLATIHEADAFGLTYDVVDDLTGKKLGRASSGTFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLH-------DDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYK 293
           DVVGLDTMAHVIKT+QD L        +DPF+ +Y TP VL  L++A +LGQKTGAGFYK
Sbjct: 241 DVVGLDTMAHVIKTLQDNLGPVGSGKVEDPFSGIYGTPPVLARLLEAKSLGQKTGAGFYK 300

Query: 294 KEGKAIKVLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDV 353
           K G+ I  LD ++  YV  G KADE+V RMLKK A ER+ LLR +   + +FLWAV RD 
Sbjct: 301 KVGRDILRLDPESMDYVAGGAKADEVVGRMLKKPAGERLSLLRHAEGAEPRFLWAVLRDQ 360

Query: 354 FHYIAVYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSA 413
           FHY AV+L  IA +A DID A+RWGFG   GPFE WQ AGW QVA W++ED+EAGKALS 
Sbjct: 361 FHYAAVHLASIAETARDIDFAMRWGFGAKQGPFELWQEAGWLQVANWIREDIEAGKALST 420

Query: 414 APLPAWVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRK 473
           APLP WVF GPVAE  GVH   GSWS + Q F+AR KLPVY RQ F   + G  A     
Sbjct: 421 APLPDWVFSGPVAEAGGVHTPEGSWSASGQKFIARRKLPVYARQHFPEDVLGANAPAFET 480

Query: 474 AGRTVEENDAVRIWVSEGQD----DVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGL 529
           AG T+ E+DA+R+W  +G +    DVL+ S K+KM+ I PDV +GL   ++LAE GYKGL
Sbjct: 481 AGTTLHEDDAIRLWTLDGANGEAGDVLIASIKTKMHAISPDVAEGLALGVELAEKGYKGL 540

Query: 530 VVWQPTSLQLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVV 589
           V+W    +        FSAGA+L++ +PAFMMGGA  IE      Q  M++++YA+VPVV
Sbjct: 541 VIWSNHEM--------FSAGADLQSMLPAFMMGGAAMIEGVEAELQKVMLKLRYAAVPVV 592

Query: 590 SAASGIALGGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAG 649
           SA  G+ALGGGCE+ ++SA RVAA+E+YIGLVEVGVGLVP  GGL   A  AA  A  + 
Sbjct: 593 SAIRGLALGGGCEMAVYSARRVAAMESYIGLVEVGVGLVPGAGGLAYIARRAAENAAKSS 652

Query: 650 STNILQFLTSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASA 709
           + ++L FL   F +AAMA V  SALE+R++GYL  SD +V N  ELL+VA NE RAL ++
Sbjct: 653 NKDLLPFLLEGFTAAAMATVGTSALESRKLGYLLDSDVVVPNKDELLFVALNEARALHAS 712

Query: 710 GYRAPLPTLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLV 769
           GYR PL  L PVAGR+G+ATIK  LVNMRDGGFIS HDF IAS IA  VCGGDV+AG+LV
Sbjct: 713 GYRPPLRRLFPVAGRNGVATIKGQLVNMRDGGFISAHDFHIASLIAGVVCGGDVDAGTLV 772

Query: 770 SEDWLLALERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           +E++L+ LERKAF  LL   KTQERIMGM+ TGKPVRN
Sbjct: 773 TEEYLMTLERKAFCALLEHPKTQERIMGMMSTGKPVRN 810


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: 1700
Number of extensions: 63
Number of successful extensions: 5
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: 810
Length adjustment: 41
Effective length of query: 766
Effective length of database: 769
Effective search space:   589054
Effective search space used:   589054
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 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