Alignments for a candidate for ech in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Stenotrophomonas chelatiphaga DSM 21508

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_057507300.1 ABB28_RS03505 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_001431535.1:WP_057507300.1
          Length = 687

 Score =  376 bits (965), Expect = e-108
 Identities = 245/684 (35%), Positives = 362/684 (52%), Gaps = 30/684 (4%)

Query: 11  VRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGAD 70
           +R D + V+ +D     +N +  +   ++  +I+++  +   +GVV  SAK   FIAGAD
Sbjct: 17  IRDDGVVVLNLDRQDANVNAMSQDVLLELGDLIERIAIDPP-KGVVIQSAKKAGFIAGAD 75

Query: 71  INMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTD 130
           +                R+GQ    ++  LP   +AAIHG CLGGG ELALAC  RV ++
Sbjct: 76  LKEFQEFDRRGTVNDAIRRGQVTYQKLAELPCPTVAAIHGHCLGGGTELALACRYRVASN 135

Query: 131 DPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVP 190
           D  T +GLPE QLG+ PG GG+ RLP+L+G   A++M+LTG+ L A  A  +GLVD VV 
Sbjct: 136 DSSTRIGLPETQLGIFPGWGGSARLPQLVGAPAAMDMMLTGRTLSASAARNIGLVDKVVA 195

Query: 191 HSILLEAAVELAKKERPSSRPLPVRERILAGPL--GRALLFKMVGKKTEHKTQG-NYPAT 247
            ++LL+ AV LA K   + RP   R    A      R LL   + K+   K +  +YPA 
Sbjct: 196 PALLLDTAVALALKG--TVRPFKQRATAWATNTWPARKLLAPQMAKQVARKARKEHYPAP 253

Query: 248 ERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGSDAPPAP 307
             ++   E    +   +  DAE RA  +LA TP ++ L  IFF +  +K     D     
Sbjct: 254 YALINTWERSGGKPVQARLDAERRAVVKLASTPTARNLIRIFFLTERLKALGSGDHG--- 310

Query: 308 LNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRRHLKA 367
           ++ V ++G G+MGG IA  +A K G  V ++D   + I+ A++ +    E KVR    + 
Sbjct: 311 IHHVHVVGAGVMGGDIAAWSAYK-GFNVTLQDREQRFIDPAMQRAQTLFEKKVRDESKRP 369

Query: 368 SERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSL 427
           +   +  A ++G     G A  DL+IEA+ EN + K+ +   +E    A  +  +NTSS+
Sbjct: 370 AVAARLQADLAGA----GAAQADLVIEAIIENPQAKRDLYQTLEPKMKADALLTTNTSSI 425

Query: 428 PIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVV 487
           P+ ++  H  RP Q  GLH+F+PV +MPLVEII H G + +T        K  GK P+ V
Sbjct: 426 PLIELRDHIQRPAQFAGLHYFNPVAQMPLVEIIHHDGMAPETERRLAAFCKALGKFPVPV 485

Query: 488 RDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKI 547
               GF VNR+L PY+ EA     +G     ID A VKFG P+GPI+LLD VG+D    +
Sbjct: 486 AGTPGFLVNRVLFPYMLEAATAYAEGIPGPVIDKAAVKFGMPMGPIELLDTVGLDVAAGV 545

Query: 548 IPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPAIYPLIGT 607
              L    G +  A    V       ++G+K+G+G Y + + GR  K +V        G 
Sbjct: 546 GEELAPFLGLQIPAALQTV----EPGKRGKKDGQGIYAW-ENGRAKKPEVPK------GY 594

Query: 608 QGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYID 667
           Q  G      + +R ++ +LNEAV C+ E V+      D G +FG GF PF GGP +YI 
Sbjct: 595 QAPG-----DLEDRLILPLLNEAVACLHEGVVADADLLDAGVIFGTGFAPFRGGPVQYIR 649

Query: 668 SLGAGEVVAIMQRLATQYGSRFTP 691
           + GA  +V  ++ L  ++G RF+P
Sbjct: 650 ATGADALVERLKVLQQRHGDRFSP 673


Lambda     K      H
   0.319    0.137    0.393 

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: 1019
Number of extensions: 54
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: 714
Length of database: 687
Length adjustment: 39
Effective length of query: 675
Effective length of database: 648
Effective search space:   437400
Effective search space used:   437400
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: 54 (25.4 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)
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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