Alignments for a candidate for ech in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Thauera aminoaromatica S2

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_004300931.1 C665_RS04225 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000310185.1:WP_004300931.1
          Length = 793

 Score =  856 bits (2212), Expect = 0.0
 Identities = 450/810 (55%), Positives = 564/810 (69%), Gaps = 20/810 (2%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MS  I++KVAVLGAGVMGAQIAAH  NA VPV+LFDLPAKEGP NG+  +A+  +KKL P
Sbjct: 1   MSRLIIRKVAVLGAGVMGAQIAAHCANADVPVILFDLPAKEGPANGVVDKALAGMKKLDP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           AP   K+ A  ++AANY  D+A L ECDLVIEAIAE+M+WK DLY KVAPHL + AIFA+
Sbjct: 61  APFAAKDRAQYVEAANYGSDLARLGECDLVIEAIAEKMEWKLDLYAKVAPHLKAGAIFAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSI AL+ G  AD +S+FCG+HFFNPPRYM LVELIP A T   +LD LEA+LTT 
Sbjct: 121 NTSGLSIEALATGMPADRRSQFCGIHFFNPPRYMPLVELIPIAATDAALLDGLEAWLTTH 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGK +VRAKDTPNF+ANRVG+FSILAV     + G+ FD VD LTG ++GR KSATFRTA
Sbjct: 181 LGKSIVRAKDTPNFVANRVGVFSILAVLHHTARLGLAFDEVDLLTGPRIGRPKSATFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDT+ HV+ TMQ TL DDP+   ++TP  L+ L+  GALGQKT  G Y+K+G+ I+
Sbjct: 241 DVVGLDTLVHVLGTMQATLPDDPWCAHFRTPEWLQALIAKGALGQKTKCGIYRKQGRQIQ 300

Query: 301 VLDAKTGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAV 359
           VLD     Y ++G +    V  +LK K+ AE+   L    +PQAQFLW++FRDVFHY AV
Sbjct: 301 VLDLHLQDYRESGGEVLPEVAEILKLKNPAEKFAQLAAHPHPQAQFLWSIFRDVFHYCAV 360

Query: 360 YLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAW 419
           +L  IA SA DIDLA+RWGFGW  GPFE WQ+AGW+ VAE +++D+  G+A+SA PLPAW
Sbjct: 361 HLGDIADSARDIDLAMRWGFGWAQGPFETWQAAGWRAVAEMIRDDIAHGRAMSAVPLPAW 420

Query: 420 VFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVE 479
           VF     E  GVHA AGS+S A  S   RS LPVYQRQ +   + G A   P   G T+ 
Sbjct: 421 VF-----ERDGVHAPAGSYSAAEDSLKPRSALPVYQRQLYPDRVLGEA---PDDRGETLW 472

Query: 480 ENDAVRIWVSEGQD-DVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538
           EN  VR+W    QD  + +VS  SKM+ +G +V+DGL  AI  AE    GLV+WQP    
Sbjct: 473 ENAGVRLWRRADQDARIGIVSITSKMHAVGEEVMDGLLEAIARAETDLDGLVIWQP---- 528

Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598
                 PF+ GANL+    A   G  + +E  V +FQ   M +K+A VPVV+A  G+ALG
Sbjct: 529 -----APFAVGANLQQVGEACRAGQFELLERMVAKFQRTSMTIKHAQVPVVAAVQGMALG 583

Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLT 658
           GGCE ++H+A RV ALE+Y+GLVE GVGL+PAGGG KE AL A   AQ A   ++  ++ 
Sbjct: 584 GGCEFVMHAAHRVFALESYVGLVEAGVGLIPAGGGSKEFALQAHALAQRAAGGDVFPYIQ 643

Query: 659 SRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT- 717
           + FQ+ AMA V+ SA EA Q+G+ +  D I+FN +E+LY A    RALA + +R  L   
Sbjct: 644 NAFQTIAMATVAKSAQEAVQLGFGRTGDDILFNANEILYAAIRRARALAESAWRPALVNP 703

Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777
            V VAGR+GIAT +  LVNM +GGFIS HD+ +A   A A+CGG+V+    VSE W+L +
Sbjct: 704 AVTVAGRNGIATCEMMLVNMAEGGFISAHDYRVAKAAATALCGGEVDTNRRVSEQWILEV 763

Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           ER  FV+LL T KTQ+RI  ML+TGKP+RN
Sbjct: 764 ERAQFVELLKTEKTQQRIAHMLETGKPLRN 793


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: 1568
Number of extensions: 58
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: 793
Length adjustment: 41
Effective length of query: 766
Effective length of database: 752
Effective search space:   576032
Effective search space used:   576032
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