Alignments for a candidate for fadB in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Dechlorosoma suillum PS

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Dsui_0318 Dsui_0318 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>FitnessBrowser__PS:Dsui_0318
          Length = 795

 Score =  852 bits (2200), Expect = 0.0
 Identities = 443/808 (54%), Positives = 558/808 (69%), Gaps = 19/808 (2%)

Query: 2   SNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPA 61
           S  IV++ AVLGAGVMGAQIAAHL NA VPVVLFDL AKEG  NGI  +A++ LKKL PA
Sbjct: 5   SKLIVRRAAVLGAGVMGAQIAAHLANADVPVVLFDLAAKEGDPNGIVKKALDGLKKLDPA 64

Query: 62  PLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATN 121
           PL  KE    I AANYE  +ALL ECDLVIEAIAE+M+WK DLY+K+APHL + AI A+N
Sbjct: 65  PLASKERLAHIDAANYEQHLALLGECDLVIEAIAEKMEWKEDLYRKIAPHLKAGAIVASN 124

Query: 122 TSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTL 181
           TSGLSI  LS    A+ ++ FCG+HFFNPPRYM LVE+I T  + P +LD+LE +L + L
Sbjct: 125 TSGLSINKLSSTVPAEKRANFCGIHFFNPPRYMPLVEIIATTDSDPAMLDRLETWLVSRL 184

Query: 182 GKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTAD 241
           GK VVRAKDTPNF+ANRVG+FSILAV    ++  + FD VD LTG K+GR KSAT+RTAD
Sbjct: 185 GKSVVRAKDTPNFVANRVGVFSILAVMHHTQRLEMGFDEVDALTGPKIGRPKSATYRTAD 244

Query: 242 VVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKV 301
           VVGLDT+AHV+KTMQDTL  DP+   ++ PA L  L++ GALGQKT  G ++K+GK I+V
Sbjct: 245 VVGLDTLAHVVKTMQDTLPGDPWHSHFQAPAWLAALIEKGALGQKTKCGIFRKQGKEIQV 304

Query: 302 LD-AKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVY 360
           LD AK      AG+ A E+   +  K+ AE+   LR S++ QAQFLWA++RDVFHY A +
Sbjct: 305 LDLAKQDYRTSAGEIAPEVAEILKIKNPAEKFAALRASSHKQAQFLWAIYRDVFHYCAFH 364

Query: 361 LEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWV 420
           LE IA +A D+D A+RWGFGW  GPFE WQ+AGWK +A  V+ D++AG A+S APLPAWV
Sbjct: 365 LESIADNARDVDFAMRWGFGWAMGPFETWQAAGWKAIAAAVQADIDAGLAMSTAPLPAWV 424

Query: 421 FEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEE 480
                    GVH  AGSWS A Q    RS LPVY RQ +   + G A   P   G TV E
Sbjct: 425 M-----ARDGVHEPAGSWSAAEQGLKPRSALPVYGRQLYPETVLGEA---PAAKGETVWE 476

Query: 481 NDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLG 540
           N  VR+W       + ++S  SKM+ IG +V+DG+  A+  AE  + GLV+W        
Sbjct: 477 NAGVRLWTHAQDPKIAILSITSKMHAIGDEVLDGVLEAVSRAERDFDGLVIWHE------ 530

Query: 541 APGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGG 600
               PF+ GANL+    A   G    +E  V +FQ   M  K+A VP V+A  G+ALGGG
Sbjct: 531 ---APFAVGANLQQVGEACAKGEFDKLEATVAKFQRASMAFKHAQVPTVAAVQGMALGGG 587

Query: 601 CELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSR 660
           CE ++H+A RV ALE+Y+GLVE GVGL+PAGGG KE A+ AA+         +  FL + 
Sbjct: 588 CEFVMHAAHRVMALESYVGLVEAGVGLIPAGGGCKEFAIRAAQFGARQAGGELFPFLQNV 647

Query: 661 FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPTL-V 719
           FQ+ AMAKV+ SALE ++MG+ + +D IVFN  ELL+VA    RA+A+AGYR PL    +
Sbjct: 648 FQTIAMAKVAKSALEVQEMGFGKEADDIVFNAQELLFVAIARARAMAAAGYRPPLRARNI 707

Query: 720 PVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALER 779
           PVAGR GIAT++  LVNM++GGFIS HD+ +A   A A+CGGDVE GS V ++WLL +ER
Sbjct: 708 PVAGRPGIATLEMMLVNMKEGGFISAHDYRVARSAAIALCGGDVEQGSRVDDEWLLTVER 767

Query: 780 KAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           + FV+LL T +TQ RI  ML+TGKP+RN
Sbjct: 768 REFVELLKTPETQARIKHMLETGKPLRN 795


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: 1525
Number of extensions: 61
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: 795
Length adjustment: 41
Effective length of query: 766
Effective length of database: 754
Effective search space:   577564
Effective search space used:   577564
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 Apr 09 2024. 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